Institute of Neurosciences and Medicine (INM)

Computational Biomedicine (INM-9)

Publications of IAS-5/INM-9

Journal Article Antalík, A. ; Levy, A. ; Kvedaravičiūtė, S. ; Johnson, S. K. ; Carrasco-Busturia, D. ; Raghavan, B.FZJ* ; Mouvet, F. ; Acocella, A. ; Das, S. ; Gavini, V. ; Mandelli, D.FZJ* ; Ippoliti, E.FZJ* ; Meloni, S. ; Carloni, P.FZJ* ; Rothlisberger, U. ; Olsen, J. M. H. (Corresponding author)
MiMiC: A high-performance framework for multiscale molecular dynamics simulations
The journal of chemical physics 161(2), 022501 (2024) [10.1063/5.0211053]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Carrasco-Busturia, D. ; Ippoliti, E.FZJ* ; Meloni, S. ; Rothlisberger, U. ; Olsen, J. M. H. (Corresponding author)
Multiscale biomolecular simulations in the exascale era
Current opinion in structural biology 86, 102821 - (2024) [10.1016/j.sbi.2024.102821]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Malapally, N. (First author)FZJ* ; Bolnykh, V. ; Suarez, E.FZJ* ; Carloni, P.FZJ* ; Lippert, T.FZJ* ; Mandelli, D. (Corresponding author)FZJ*
3D DFT by block tensor-matrix multiplication via a modified Cannon's algorithm: Implementation and scaling on distributed-memory clusters with fat tree networks
Journal of parallel and distributed computing 193, 104945 - (2024) [10.1016/j.jpdc.2024.104945]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Abstract Bondar, A.-N.FZJ* ; Hristova, K. ; Wimley, W. C.
Mechanism by which water interactions stabilize a pH-dependent membrane pore
2024Biophysical Society Meeting, PhiladelphiaPhiladelphia, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.2011]2024 Fulltext BibTeX | EndNote: XML, Text | RIS

Abstract Kelly, M. S. ; Capelli, R. ; Kahawatte, S. ; Wijethunga, H. ; Carloni, P.FZJ* ; Dima, R. I.
Optimizing biophysical predictor selection for katanin allosteric transitions via metadynamics and machine learning
2024Biophysical Society Meeting, PhiladelphiaPhiladelphia, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024) [10.1016/j.bpj.2023.11.1698]2024 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Beck, T. L. (Corresponding author) ; Carloni, P.FZJ* ; Asthagiri, D. N.
All-Atom Biomolecular Simulation in the Exascale Era
Journal of chemical theory and computation 20(5), 1777 - 1782 (2024) [10.1021/acs.jctc.3c01276]2024 Embargoed OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Dmitrieva, N.FZJ* ; Gholami, S.FZJ* ; Alleva, C. ; Carloni, P.FZJ* ; Alfonso-Prieto, M.FZJ* ; Fahlke, C. (Corresponding author)FZJ*
Transport mechanism of DgoT, a bacterial homolog of SLC17 organic anion transporters
bioRxiv beta (2024) [10.1101/2024.02.07.579339]2024 OpenAccess Files Fulltext BibTeX | EndNote: XML, Text | RIS

Preprint Pirona, L. ; Ballabio, F. ; Alfonso-Prieto, M.FZJ* ; Capelli, R. (Corresponding author)
Calcium-driven In Silico Inactivation of a Human Olfactory Receptor
bioRxiv beta (2024) [10.1101/2024.01.31.578070]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Alfonso-Prieto, M. (Corresponding author)FZJ* ; Müller, N.FZJ* ; Sergeeva, O. A. ; Navarini, L. ; Carloni, P.FZJ*
Molecular insights into the neuroprotective effects of chlorogenic acids mediated by the peroxisome proliferator-activated receptor PPARalpha
2024Biophysical Society Meeting, PhiladelphiaPhiladelphia, USA, 10 Feb 2024 - 14 Feb 20242024-02-102024-02-14 (2024)2024 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Dmitrieva, N.FZJ* ; Gholami, S.FZJ* ; Alleva, C. ; Alfonso-Prieto, M.FZJ* ; Carloni, P.FZJ* ; Fahlke, C. M. (Corresponding author)FZJ*
Transport mechanisms of DgoT—a bacterial homolog of organic anion transporters
Biophysical journal 123(3), 116a - (2024) [10.1016/j.bpj.2023.11.811]2024 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pirona, L. ; Ballabio, F. ; Alfonso-Prieto, M.FZJ* ; Capelli, R. (Corresponding author)
Calcium-Driven In Silico Inactivation of a Human Olfactory Receptor
Journal of chemical information and modeling 64(8), 2971–2978 (2024) [10.1021/acs.jcim.4c00249]2024 OpenAccess Files Fulltext BibTeX | EndNote: XML, Text | RIS

Contribution to a book Fahlke, C. (Editor)FZJ* ; Asgharpour, S. ; Chi, L. A. ; Spehr, M.RWTH* ; Carloni, P. (Corresponding author)FZJ* ; Alfonso-Prieto, M. (Corresponding author)FZJ*
Fluoride Transport and Inhibition Across CLC Transporters
2024Anion Channels and Transporters / Fahlke, Christoph (Editor) ; Cham : Springer International Publishing, 2024, Chapter 593 ; ISSN: 0171-2004=1865-0325 ; ISBN: 978-3-031-51345-9=978-3-031-51346-6 ; doi:10.1007/978-3-031-51346-6 Cham : Springer International Publishing, Handbook of Experimental Pharmacology 283, 81 - 100 (2024) [10.1007/164_2022_593]2024 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Albani, S.FZJ* ; Costanzi, E. ; Hoang, G. L.FZJ* ; Kuzikov, M. ; Frings, M. ; Ansari, N. ; Demitri, N. ; Nguyen, T. T. ; Rizzi, V. ; Schulz, J. B.FZJ* ; Bolm, C. ; Zaliani, A. ; Carloni, P. (Corresponding author)FZJ* ; Storici, P. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ*
Unexpected Single-Ligand Occupancy and Negative Cooperativity in the SARS-CoV-2 Main Protease
Journal of chemical information and modeling 64(3), 892–904 (2024) [10.1021/acs.jcim.3c01497]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Mazzei, L. (Corresponding author) ; Paul, A. ; Cianci, M. ; Devodier, M.FZJ* ; Mandelli, D.FZJ* ; Carloni, P.FZJ* ; Ciurli, S.
Kinetic and structural details of urease inactivation by thiuram disulphides
Journal of inorganic biochemistry 250, 112398 - (2024) [10.1016/j.jinorgbio.2023.112398]2024 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Faraji, E. (Corresponding author)FZJ* ; Nourmandipour, A. ; Mancini, S. ; Pettini, M. ; Franzosi, R.
Routing a quantum state in a bio-inspired network
Quantum information processing 22(7), 266 (2023) [10.1007/s11128-023-03942-1]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Conference Presentation (After Call) Neumaier, B. (Corresponding author)FZJ* ; Cologni, R.FZJ* ; Holschbach, M.FZJ* ; Bier, D.FZJ* ; Carloni, P.FZJ*
18F-Labelled inhibitors for targeting of IDH1 mutant gliomas
202325th International Symposium on Radiopharmaceutical Sciences, ISRS2023, Honolulu, USAHonolulu, USA, USA, 22 May 2023 - 26 May 20232023-05-222023-05-26 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bondar, A.-N. (Corresponding author)FZJ* ; Barboiu, M.
Protons at bio-interfaces
Biochimica et biophysica acta / Biomembranes 1865(4), 184139 - (2023) [10.1016/j.bbamem.2023.184139]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Alfonso-Prieto, M. (Corresponding author)FZJ* ; Capelli, R. (Corresponding author)
Machine Learning-based Modeling of Olfactory Receptors in their Inactive State: Human OR51E2 as a Case Study
bioRxiv beta (2023) [10.1101/2023.02.22.529484]2023 OpenAccess Files Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Dmitrieva, N.FZJ* ; Alleva, C. ; Alfonso-Prieto, M.FZJ* ; Carloni, P.FZJ* ; Fahlke, C. M. (Corresponding author)FZJ*
Exploring the transport cycle of DgoT, a bacterial homolog of human vesicular glutamate transporters
Biophysical journal 122(3), 231a - (2023) [10.1016/j.bpj.2022.11.1363]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Saliminasab, M. ; Yamazaki, Y. ; Palmateer, A. ; Harris, A. ; Schubert, L. ; Langner, P. ; Heberle, J. ; Bondar, A.-N. (Corresponding author)FZJ* ; Brown, L. S.
A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins
The journal of physical chemistry / B 127(37), 7872 - 7886 (2023) [10.1021/acs.jpcb.3c04032]2023 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Lešnik, S. ; Bren, U. ; Domratcheva, T. ; Bondar, A.-N. (Corresponding author)FZJ*
Fentanyl and the Fluorinated Fentanyl Derivative NFEPP Elicit Distinct Hydrogen-Bond Dynamics of the Opioid Receptor
Journal of chemical information and modeling 63(15), 4732 - 4748 (2023) [10.1021/acs.jcim.3c00197]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Jain, H. ; Karathanou, K. ; Bondar, A.-N. (Corresponding author)FZJ*
Graph-Based Analyses of Dynamic Water-Mediated Hydrogen-Bond Networks in Phosphatidylserine: Cholesterol Membranes
Biomolecules 13(8), 1238 - (2023) [10.3390/biom13081238]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kapur, B. ; Baldessari, F. ; Lazaratos, M. ; Nar, H. ; Schnapp, G. ; Giorgetti, A.FZJ* ; Bondar, A.-N. (Corresponding author)FZJ*
Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68
Computational and structural biotechnology journal 21, 4370 - 4384 (2023) [10.1016/j.csbj.2023.08.034]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Morizumi, T. ; Kim, K. ; Li, H.FZJ* ; Govorunova, E. G. ; Sineshchekov, O. A. ; Wang, Y. ; Zheng, L. ; Bertalan, É. ; Bondar, A.-N.FZJ* ; Askari, A. ; Brown, L. S. ; Spudich, J. L. ; Ernst, O. P. (Corresponding author)
Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K+ and Na+ selectivities
Nature Communications 14(1), 4365 (2023) [10.1038/s41467-023-40041-2]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Oliva, F. ; Musiani, F. ; Giorgetti, A.FZJ* ; De Rubeis, S. ; Sorokina, O. ; Armstrong, D. J. ; Carloni, P.FZJ* ; Ruggerone, P. (Corresponding author)
Modelling eNvironment for Isoforms (MoNvIso): A general platform to predict structural determinants of protein isoforms in genetic diseases
Frontiers in Chemistry 10, 1059593 (2023) [10.3389/fchem.2022.1059593]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Ribeiro, R. P. ; Giorgetti, A. (Corresponding author)FZJ*
pyGOMoDo: GPCRs modeling and docking with python
Bioinformatics 39(5), btad294 (2023) [10.1093/bioinformatics/btad294]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Nicoli, A. ; Haag, F. ; Marcinek, P. ; He, R. ; Kreißl, J. ; Stein, J. ; Marchetto, A.FZJ* ; Dunkel, A. ; Hofmann, T. ; Krautwurst, D. (Corresponding author) ; Di Pizio, A. (Corresponding author)
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1
Journal of chemical information and modeling 63(7), 2014 - 2029 (2023) [10.1021/acs.jcim.2c00752]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Yildiz, C. B. ; Kundu, T. ; Gehrmann, J. ; Koesling, J. ; Ravaei, A. ; Wolff, P. ; Kraft, F. ; Maié, T. ; Jakovcevski, M. ; Pensold, D. ; Zimmermann, O. (Corresponding author)FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Costa, I. G. (Corresponding author) ; Zimmer-Bensch, G. (Corresponding author)
EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter
Epigenetics & chromatin 16(1), 42 (2023) [10.1186/s13072-023-00516-4]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Paulikat, M.FZJ* ; Piccini, G. ; Ippoliti, E.FZJ* ; Rossetti, G.FZJ* ; Arnesano, F. ; Carloni, P. (Corresponding author)FZJ*
Physical Chemistry of Chloroquine Permeation through the Cell Membrane with Atomistic Detail
Journal of chemical information and modeling 63(22), 7124 - 7132 (2023) [10.1021/acs.jcim.3c01363]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Rizzi, A. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Parrinello, M. (Corresponding author)
Free energies at QM accuracy from force fields via multimap targeted estimation
Proceedings of the National Academy of Sciences of the United States of America 120(40), e2304308120 (2023) [10.1073/pnas.2304308120]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bonati, L. (Corresponding author) ; Trizio, E. ; Rizzi, A.FZJ* ; Parrinello, M.
A unified framework for machine learning collective variables for enhanced sampling simulations: mlcolvar
The journal of chemical physics 159(1), 014801 (2023) [10.1063/5.0156343]2023 Embargoed OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kranjc Pietrucci, A. (Corresponding author)FZJ* ; Narwani, T. J. ; Abby, S. S. ; de Brevern, A. G. (Corresponding author)
Structural Space of the Duffy Antigen/Receptor for Chemokines’ Intrinsically Disordered Ectodomain 1 Explored by Temperature Replica-Exchange Molecular Dynamics Simulations
International journal of molecular sciences 24(17), 13280 - (2023) [10.3390/ijms241713280]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Joseph, B. P.FZJ* ; Weber, V.FZJ* ; Knüpfer, L. ; Giorgetti, A.FZJ* ; Alfonso-Prieto, M.FZJ* ; Krauß, S. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ* ; Rossetti, G.FZJ*
Low Molecular Weight Inhibitors Targeting the RNA-Binding Protein HuR
International journal of molecular sciences 24(17), 13127 - (2023) [10.3390/ijms241713127]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Zhang, J. ; Song, D. ; Schackert, F. K.FZJ* ; Li, J. ; Xiang, S. ; Tian, C. ; Gong, W. ; Carloni, P.FZJ* ; Alfonso-Prieto, M.FZJ* ; Shi, C. (Corresponding author)
Fluoride permeation mechanism of the Fluc channel in liposomes revealed by solid-state NMR
Science advances 9(34), eadg9709 (2023) [10.1126/sciadv.adg9709]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Goßen, J.FZJ* ; Ribeiro, R. P.FZJ* ; Bier, D.FZJ* ; Neumaier, B.FZJ* ; Carloni, P.FZJ* ; Giorgetti, A.FZJ* ; Rossetti, G. (Corresponding author)FZJ*
AI-based identification of therapeutic agents targeting GPCRs: introducing ligand type classifiers and systems biology
Chemical science 14(32), 8651-8661 (2023) [10.1039/D3SC02352D]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Raghavan, B. (First author)FZJ* ; Paulikat, M. (First author)FZJ* ; Ahmad, K. ; Callea, L. ; Rizzi, A.FZJ* ; Ippoliti, E.FZJ* ; Mandelli, D. (Corresponding author)FZJ* ; Bonati, L. ; De Vivo, M. ; Carloni, P. (Corresponding author)FZJ*
Drug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations
Journal of chemical information and modeling 63(12), 3647 - 3658 (2023) [10.1021/acs.jcim.3c00557]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Zuo, K.FZJ* ; Kranjc, A.FZJ* ; Capelli, R. ; Rossetti, G.FZJ* ; Nechushtai, R. ; Carloni, P. (Corresponding author)FZJ*
Metadynamics simulations of ligands binding to protein surfaces: a novel tool for rational drug design
Physical chemistry, chemical physics 25(20), 13819 - 13824 (2023) [10.1039/D3CP01388J]2023 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M. (Corresponding author)FZJ* ; Capelli, R. (Corresponding author)
Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study
Journal of chemical information and modeling 63(10), 2911 - 2917 (2023) [10.1021/acs.jcim.3c00380]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Preprint Dorn, A.FZJ* ; de Bruyn, E.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Fernandez, C. ; Outeiro, T. F. ; Schulz, J. B.FZJ* ; Carloni, P.FZJ*
Impact of Phosphorylation on alpha-Synuclein Structural Determinants
bioRxiv beta (2023) [10.1101/2023.03.10.531864]2023 Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article de Bruyn, E. (First author)FZJ* ; Dorn, A.FZJ* ; Zimmermann, O. (Corresponding author)FZJ* ; Rossetti, G. (Corresponding author)FZJ*
SPEADI: Accelerated Analysis of IDP-Ion Interactions from MD-Trajectories
Biology 12(4), 581 - (2023) [10.3390/biology12040581] special issue: "Intrinsically Disordered Proteins Interactions with Their Molecular Environment at the Crossroad between Theory and Experiments"2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Preprint Malapally, N.FZJ* ; Bolnykh, V. ; Suarez, E.FZJ* ; Carloni, P.FZJ* ; Lippert, T.FZJ* ; Mandelli, D. (Corresponding author)FZJ*
Scalability of 3D-DFT by block tensor-matrix multiplication on the JUWELS Cluster
Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (Invited) Tan, Z. (Corresponding author)FZJ*
Quasi-two-dimensional protein dispersions:From monolayers with competing interactions to a protein-membrane-cytosol model of neuronal signal transduction
2023Vortrag im Seminar Statistische Physik weicher Materie und biologischer Systeme, TU BerlinBerlin, TU Berlin, Germany, 17 Mar 2023 - 17 Mar 20232023-03-172023-03-17 BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M.FZJ* ; Cuxart, I. ; Potocki-Véronèse, G. ; André, I. (Corresponding author) ; Rovira, C. (Corresponding author)
Substrate-Assisted Mechanism for the Degradation of N -Glycans by a Gut Bacterial Mannoside Phosphorylase
ACS catalysis 13, 4283 - 4289 (2023) [10.1021/acscatal.3c00451]2023 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Raghavan, B.FZJ* ; Schackert, F. K.FZJ* ; Levy, A. ; Johnson, S. K. ; Ippoliti, E.FZJ* ; Mandelli, D. (Corresponding author)FZJ* ; Olsen, J. M. H. ; Rothlisberger, U. ; Carloni, P. (Corresponding author)FZJ*
MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations
Journal of chemical information and modeling 63(5), 1406 - 1412 (2023) [10.1021/acs.jcim.2c01620]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schackert, F. K.FZJ* ; Biedermann, J.Extern* ; Abdolvand, S.Extern* ; Minniberger, S.Extern* ; Song, C. ; Plested, A. J. R.Extern* ; Carloni, P. (Corresponding author)FZJ* ; Sun, H. (Corresponding author)Extern*
Mechanism of Calcium Permeation in a Glutamate Receptor Ion Channel
Journal of chemical information and modeling 63(4), 1293 - 1300 (2023) [10.1021/acs.jcim.2c01494]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ortiz, C. ; Klein, S. ; Reul, W. H. ; Magdaleno, F. ; Gröschl, S. ; Dietrich, P. ; Schierwagen, R. ; Uschner, F. E. ; Torres, S. ; Hieber, C. ; Meier, C. ; Kraus, N. ; Tyc, O. ; Brol, M. ; Zeuzem, S. ; Welsch, C. ; Poglitsch, M. ; Hellerbrand, C. ; Alfonso-Prieto, M.FZJ* ; Mira, F. ; Keller, U. a. d. ; Tetzner, A. ; Moore, A. ; Walther, T. ; Trebicka, J. (Corresponding author)
Neprilysin-dependent neuropeptide Y cleavage in the liver promotes fibrosis by blocking NPY-receptor 1
Cell reports 42(2), 112059 (2023) [10.1016/j.celrep.2023.112059]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Mueller, N. P. F.FZJ* ; Carloni, P.FZJ* ; Alfonso-Prieto, M. (Corresponding author)FZJ*
Molecular determinants of acrylamide neurotoxicity through covalent docking
Frontiers in pharmacology 14, 1125871 (2023) [10.3389/fphar.2023.1125871]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bertalan, É. ; Bondar, A.-N. (Corresponding author)FZJ*
Graphs of protein-water hydrogen bond networks to dissect structural movies of ion-transfer microbial rhodopsins
Frontiers in Chemistry 10, 1075648 (2023) [10.3389/fchem.2022.1075648]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zuo, K.FZJ* ; Capelli, R. ; Rossetti, G.FZJ* ; Nechushtai, R. ; Carloni, P. (Corresponding author)FZJ*
Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET
Journal of chemical information and modeling 63(2), 643 - 654 (2023) [10.1021/acs.jcim.2c01280]2023 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article van Keulen, S. C. ; Martin, J. ; Colizzi, F. ; Frezza, E. ; Trpevski, D. ; Diaz, N. C. ; Vidossich, P.Extern* ; Rothlisberger, U. (Corresponding author) ; Hellgren Kotaleski, J. (Corresponding author) ; Wade, R. C. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Multiscale molecular simulations to investigate adenylyl cyclase‐based signaling in the brain
Wiley interdisciplinary reviews / Computational Molecular Science 13(1), e1623 (2023) [10.1002/wcms.1623]2023 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Palomino-Hernandez, O.FZJ*RWTH* ; Santambrogio, C. ; Rossetti, G.FZJ* ; Fernandez, C. O.Extern* ; Grandori, R. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ*
Molecular Dynamics-Assisted Interpretation of Experimentally Determined Intrinsically Disordered Protein Conformational Components: The Case of Human α-Synuclein
The journal of physical chemistry <Washington, DC> / B 126(20), 3632 - 3639 (2022) [10.1021/acs.jpcb.1c10954]2022 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Marjault, H.-B. ; Yang-Sung, S. ; Zuo, K.FZJ* ; Carloni, P.FZJ* ; Mittler, R. ; Nechushtai, R. (Corresponding author)
Structure-Based Screening Reveals a Ligand That Stabilizes the [2Fe-2S] Clusters of Human mitoNEET and Reduces Ovarian Cancer Cell Proliferation
The journal of physical chemistry <Washington, DC> / B 126(46), 9559 - 9565 (2022) [10.1021/acs.jpcb.2c05728]2022 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Karathanou, K. ; Bondar, A.-N. (Corresponding author)FZJ*
Algorithm to catalogue topologies of dynamic lipid hydrogen-bond networks
Biochimica et biophysica acta / Biomembranes 1864(4), 183859 - (2022) [10.1016/j.bbamem.2022.183859]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bondar, A.-N. (Corresponding author)FZJ*
Graphs of Hydrogen-Bond Networks to Dissect Protein Conformational Dynamics
The journal of physical chemistry <Washington, DC> / B 126(22), 3973 - 3984 (2022) [10.1021/acs.jpcb.2c00200]2022 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lazaratos, M. ; Siemers, M. ; Brown, L. S. ; Bondar, A.-N. (Corresponding author)FZJ*
Conserved hydrogen-bond motifs of membrane transporters and receptors
Biochimica et biophysica acta / Biomembranes 1864(6), 183896 - (2022) [10.1016/j.bbamem.2022.183896]2022 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bondar, A.-N. (Corresponding author)FZJ*
Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters
Advances in protein chemistry and structural biology 128, 199-238 (2022) [10.1016/bs.apcsb.2021.09.002]2022 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Govorunova, E. G. ; Sineshchekov, O. A. ; Brown, L. S. ; Bondar, A.-N.FZJ* ; Spudich, J. L. (Corresponding author)
Structural Foundations of Potassium Selectivity in Channelrhodopsins
mBio 13(6), e03039-22 (2022) [10.1128/mbio.03039-22]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Krishnamurthy, S. ; Sardis, M.-F. ; Eleftheriadis, N. ; Chatzi, K. E. ; Smit, J. H. ; Karathanou, K. ; Gouridis, G. ; Portaliou, A. G. ; Bondar, A.-N.FZJ* ; Karamanou, S. ; Economou, A. (Corresponding author)
Preproteins couple the intrinsic dynamics of SecA to its ATPase cycle to translocate via a catch and release mechanism
Cell reports 38(6), 110346 - (2022) [10.1016/j.celrep.2022.110346]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Paulikat, M.FZJ* ; Aranda, J. ; Ippoliti, E.FZJ* ; Orozco, M. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A Quantum Mechanics/Molecular Mechanics Study
The journal of physical chemistry letters 13, 12004 - 12010 (2022) [10.1021/acs.jpclett.2c03100]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings/Contribution to a book Chiariello, G. (Corresponding author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Ippoliti, E.FZJ*
Molecular Origin of the Unusual Proton/Fluoride Stoichiometry of CLC-Type Fluoride Transporters
2022NIC Symposium 2022 Proceedings
NIC Symposium, JülichJülich, Germany, 29 Sep 2022 - 30 Sep 20222022-09-292022-09-30 Jülich : Forschungszentrum Jülich GmbH Zentralbibliothek, Verlag, Publication Series of the John von Neumann Institute for Computing (NIC) NIC Series 51 450, 189-198 (2022)2022 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L. (Corresponding author)FZJ* ; Capelli, R. (Corresponding author) ; Bel-Hadj-Aissa, G. (Corresponding author) ; Pettini, M. (Corresponding author)
Topological origin of the protein folding transition
Physical review / E 106(5), 054134 (2022) [10.1103/PhysRevE.106.054134]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Dhont, J. K. G.FZJ* ; Naegele, G.FZJ*
Quasi-two-dimensional clustering of proteins with competitive interactions: Phase diagram and structural properties
2022NIC Symposium 2022, JülichJülich, Germany, 29 Sep 2022 - 30 Sep 20222022-09-292022-09-30 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Qi, K. ; Dhont, J. K. G.FZJ* ; Naegele, G.FZJ*
Mesoscale hydrodynamic modeling of G-protein coupled receptors diffusion
2022GPCR CECAM Workshop: Understanding function of G-Protein Coupled Receptors by atomistic and multiscale simulations, LuganoLugano, Switzerland, 12 Sep 2022 - 14 Sep 20222022-09-122022-09-14 BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Qi, K. ; Dhont, J. K. G.FZJ* ; Winkler, R. G.FZJ* ; Naegele, G.FZJ*
An efficient multiparticle collision dynamics approach to membrane protein diffusion
202236th European Colloid & Interface Society Conference, ChaniaChania, Greece, 4 Sep 2022 - 9 Sep 20222022-09-042022-09-09 BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (After Call) Tan, Z. (Corresponding author)FZJ* ; Naegele, G.FZJ*
Non-Gaussian diffusion in quasi-two-dimensional SALR dispersions
2022IBI-4 Group Seminar, GermanyGermany, 25 Oct 20222022-10-25 BibTeX | EndNote: XML, Text | RIS

Journal Article Buratti, F. A. ; Boeffinger, N. ; Garro, H. A. ; Flores, J. S. ; Hita, F. J. ; Gonçalves, P. d. C. ; Copello, F. d. R. ; Lizarraga, L. ; Rossetti, G.FZJ* ; Carloni, P.FZJ* ; Zweckstetter, M. ; Outeiro, T. F. ; Eimer, S. ; Griesinger, C. ; Fernández, C. O. (Corresponding author)
Aromaticity at position 39 in α‐synuclein: A modulator of amyloid fibril assembly and membrane‐bound conformations
Protein science 31(7), e4360 (2022) [10.1002/pro.4360]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Chi, L. A. (Corresponding author) ; Asgharpour, S. (Contributor)FZJ* ; Correa-Basurto, J. ; Bandala, C. R. ; Martínez-Archundia, M. (Corresponding author)
Unveiling the G4-PAMAM capacity to bind and protect Ang-(1-7) bioactive peptide by molecular dynamics simulations
Journal of computer aided molecular design 36(9), 653 - 675 (2022) [10.1007/s10822-022-00470-5]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Other) Cologni, R. (Corresponding author)FZJ* ; Ermert, J.FZJ* ; Carloni, P.FZJ* ; Neumaier, B. (Corresponding author)FZJ* ; Holschbach, M.FZJ*
18F-Labelled probes for non-invasive assessment of the IDH genotype in glioma patients
202260. Jahrestagung der Deutschen Gesellschaft für Nuklearmedizin, LeipzigLeipzig, Germany, 27 Apr 2022 - 30 Apr 20222022-04-272022-04-30 [10.1055/s-0042-1746026] BibTeX | EndNote: XML, Text | RIS

Journal Article Ghanem, S. S. ; Majbour, N. K. ; Vaikath, N. N. ; Ardah, M. T. ; Erskine, D. ; Jensen, N. M. ; Fayyad, M. ; Sudhakaran, I. P. ; Vasili, E. ; Melachroinou, K. ; Abdi, I. Y. ; Poggiolini, I. ; Santos, P. ; Dorn, A.FZJ* ; Carloni, P.FZJ* ; Vekrellis, K. ; Attems, J. ; McKeith, I. ; Outeiro, T. F. ; Jensen, P. H. ; El-Agnaf, O. M. A. (Corresponding author)
α-Synuclein phosphorylation at serine 129 occurs after initial protein deposition and inhibits seeded fibril formation and toxicity
Proceedings of the National Academy of Sciences of the United States of America 119(15), e2109617119 (2022) [10.1073/pnas.2109617119]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L. (Corresponding author)FZJ*
On the derivation of a Nonlinear Generalized Langevin Equation
Journal of physics communications 6(1), 015002 - (2022) [10.1088/2399-6528/ac438d]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kirsch, T. (Corresponding author) ; Olsen, J. M. H. ; Bolnykh, V.FZJ* ; Meloni, S. ; Ippoliti, E.FZJ* ; Rothlisberger, U. ; Cascella, M. ; Gauss, J.
Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC
Journal of chemical theory and computation 18(1), 13 - 24 (2022) [10.1021/acs.jctc.1c00878]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bondar, A.-N. (Corresponding author)FZJ* ; Alfonso-Prieto, M.FZJ*
Hydrogen-bond networks for proton couplings in G-Protein coupled receptors
Frontiers in physics 10, 963716 (2022) [10.3389/fphy.2022.963716]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bondar, A.-N. (Corresponding author)FZJ*
Interplay between local protein interactions and water bridging of a proton antenna carboxylate cluster
Biochimica et biophysica acta / Biomembranes 1864(12), 184052 (2022) [10.1016/j.bbamem.2022.184052]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Colini Baldeschi, A. ; Zattoni, M. ; Vanni, S. ; Nikolic, L. ; Ferracin, C. ; La Sala, G. ; Summa, M. ; Bertorelli, R. ; Bertozzi, S. M. ; Giachin, G. ; Carloni, P.FZJ* ; Bolognesi, M. L. ; De Vivo, M. ; Legname, G. (Corresponding author)
Innovative Non-PrP-Targeted Drug Strategy Designed to Enhance Prion Clearance
Journal of medicinal chemistry 65(13), 8998 - 9010 (2022) [10.1021/acs.jmedchem.2c00205]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lai, H. T. T. ; Nguyen, L. H. ; Phan, A. D. ; Kranjc Pietrucci, A. (Corresponding author)FZJ* ; Nguyen, T. T. (Corresponding author) ; Nguyen-Manh, D.
A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling
Journal of molecular modeling 28(10), 305 (2022) [10.1007/s00894-022-05231-7]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ahmad, K.FZJ* ; Rizzi, A.FZJ* ; Capelli, R. ; Mandelli, D.FZJ* ; Lyu, W. ; Carloni, P. (Corresponding author)FZJ*
Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective
Frontiers in molecular biosciences 9, 899805 (2022) [10.3389/fmolb.2022.899805]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sergeeva, O. A. (Corresponding author) ; Mazur, K. ; Reiner-Link, D. ; Lutsenko, K. ; Haas, H. L. ; Alfonso-Prieto, M.FZJ* ; Stark, H.
OLHA (N-oleoylhistamine) modulates activity of mouse brain histaminergic neurons
Neuropharmacology 215, 109167 (2022) [10.1016/j.neuropharm.2022.109167]2022 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L. (Corresponding author)FZJ*
The geometric theory of phase transitions
Journal of physics / A 55(27), 27LT01 - (2022) [10.1088/1751-8121/ac717d]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Winkler, R. G.FZJ* ; Naegele, G.FZJ*
An efficient multiparticle collision dynamics (MPC) approach to immiscible binary fluids: Hydrodynamics and application to membrane protein diffusion
2022RSCPoster Twitter Conference, OnlineOnline, UK, 1 Mar 2022 - 2 Mar 20222022-03-012022-03-02 Fulltext BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Naegele, G.FZJ* ; Winkler, R. G.FZJ*
An efficient multiparticle collision dynamics approach (MPC) to immiscible binary fluids: Hydrodynamics and application to membrane protein diffusion
2022SoftComp Annual Meeting 2022, SalernoSalerno, Italy, 17 May 2022 - 19 May 20222022-05-172022-05-19 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Winkler, R. G.FZJ* ; Naegele, G.FZJ*
An efficient multiparticle collision dynamics approach to immiscible binary fluids: Hydrodynamics and application to membrane protein diffusion
2022APS March Meeting 2022, Chicago/OnlineChicago/Online, Germany, 14 Mar 2022 - 18 Mar 20222022-03-142022-03-18 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Marjault, H.-B. ; Karmi, O. ; Zuo, K. ; Michaeli, D. ; Eisenberg-Domovich, Y. ; Rossetti, G.FZJ* ; de Chassey, B. ; Vonderscher, J. ; Cabantchik, I. ; Carloni, P.FZJ* ; Mittler, R. ; Livnah, O. ; Meldrum, E. ; Nechushtai, R. (Corresponding author)
An anti-diabetic drug targets NEET (CISD) proteins through destabilization of their [2Fe-2S] clusters
Communications biology 5(1), 437 (2022) [10.1038/s42003-022-03393-x]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Hoang Gia, L.FZJ* ; Goßen, J. ; Capelli, R. (Corresponding author) ; Nguyen, T. T. ; Sun, Z. ; Zuo, K.FZJ* ; Schulz, J. B.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Carloni, P.FZJ*
Multiple Poses and Thermodynamics of Ligands Targeting Protein Surfaces: The Case of Furosemide Binding to mitoNEET in Aqueous Solution
Frontiers in cell and developmental biology 10, 886568 (2022) [10.3389/fcell.2022.886568]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Körner, J. ; Albani, S.FZJ* ; Vishal Sudha Bhagavath Eswaran ; Röhl, A. B. ; Rossetti, G. (Corresponding author)FZJ* ; Lampert, A. (Corresponding author)
Sodium channels and local anesthetics – old friends with new perspectives
Frontiers in pharmacology 13, 837088 (2022) [10.3389/fphar.2022.837088]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Margreiter, M. A. ; Witzenberger, M. ; Wasser, Y. ; Davydova, E. ; Janowski, R. ; Metz, J. ; Habib, P. ; Sahnoun, S. E. M. ; Sobisch, C. ; Poma, B. ; Palomino-Hernandez, O. ; Wagner, M. ; Carell, T. ; Shah, N. J.FZJ* ; Schulz, J. B.FZJ* ; Niessing, D. ; Voigt, A. ; Rossetti, G. (Corresponding author)FZJ*
Small-molecule modulators of TRMT2A decrease PolyQ aggregation and PolyQ-induced cell death
Computational and structural biotechnology journal 20, 443 - 458 (2022) [10.1016/j.csbj.2021.12.029]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Meyer, M. ; Jurek, B. ; Alfonso-Prieto, M.FZJ* ; Ribeiro, R.FZJ* ; Milenkovic, V. M. ; Winter, J. ; Hoffmann, P. ; Wetzel, C. H. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Neumann, I. D. (Corresponding author)
Structure-function relationships of the disease-linked A218T oxytocin receptor variant
Molecular psychiatry 27, 907–917 (2022) [10.1038/s41380-021-01241-8]2022 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lešnik, S. ; Bertalan, É. ; Bren, U. ; Bondar, A.-N. (Corresponding author)FZJ*
Opioid Receptors and Protonation-Coupled Binding of Opioid Drugs
International journal of molecular sciences 22(24), 13353 - (2021) [10.3390/ijms222413353]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bertalan, É. ; Lesca, E. ; Schertler, G. F. X. ; Bondar, A.-N. (Corresponding author)FZJ*
C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
Journal of chemical information and modeling 61(11), 5692 - 5707 (2021) [10.1021/acs.jcim.1c00827]2021 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Toledo, M. A. S. ; Gatz, M. ; Sontag, S. ; Gleixner, K. V. ; Eisenwort, G. ; Feldberg, K. ; Hamouda, A. E. I. ; Kluge, F. ; Guareschi, R.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Sechi, A. S. ; Dufva, O. M. J. ; Mustjoki, S. M. ; Maurer, A. ; Schüler, H. M. ; Goetzke, R. ; Braunschweig, T. ; Kaiser, A. ; Panse, J. ; Jawhar, M. ; Reiter, A. ; Hilberg, F. ; Ettmayer, P. ; Wagner, W. ; Koschmieder, S. ; Brümmendorf, T. H. ; Valent, P. ; Chatain, N. ; Zenke, M.
Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis
Blood 137(15), 2070 - 2084 (2021) [10.1182/blood.2019004509]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sorokina, O. (Corresponding author)Extern* ; Mclean, C. (Corresponding author)Extern* ; Croning, M. D. R.Extern* ; Heil, K. F.Extern* ; Wysocka, E.Extern* ; He, X.Extern* ; Sterratt, D.Extern* ; Grant, S. G. N.Extern* ; Simpson, T. I.Extern* ; Armstrong, J. D.FZJ*
A unified resource and configurable model of the synapse proteome and its role in disease
Scientific reports 11(1), 9967 (2021) [10.1038/s41598-021-88945-7]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sena, D. M. (Corresponding author)Extern* ; Cong, X.Extern* ; Giorgetti, A. (Corresponding author)FZJ*
Ligand based conformational space studies of the μ-opioid receptor
Biochimica et biophysica acta / General subjects 1865(3), 129838 - (2021) [10.1016/j.bbagen.2020.129838]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Micheli, P.Extern* ; Ribeiro, R. (Corresponding author)FZJ* ; Giorgetti, A. (Corresponding author)FZJ*
A Mechanistic Model of NMDA and AMPA Receptor-Mediated Synaptic Transmission in Individual Hippocampal CA3-CA1 Synapses: A Computational Multiscale Approach
International journal of molecular sciences 22(4), 1536 - (2021) [10.3390/ijms22041536]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maggi, L. (Corresponding author)FZJ*
How super-localization affects vibrational energy exchange process in proteins
Physica / A 562, 125325 - (2021) [10.1016/j.physa.2020.125325]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kuzikov, M. (Corresponding author)Extern* ; Costanzi, E.Extern* ; Reinshagen, J.Extern* ; Esposito, F.Extern* ; Vangeel, L.Extern* ; Wolf, M.Extern* ; Ellinger, B.Extern* ; Claussen, C.Extern* ; Geisslinger, G.Extern* ; Corona, A. ; Iaconis, D.Extern* ; Talarico, C.Extern* ; Manelfi, C.Extern* ; Cannalire, R.Extern* ; Rossetti, G.FZJ* ; Gossen, J.FZJ* ; Albani, S.FZJ* ; Musiani, F.Extern* ; Herzog, K.Extern* ; Ye, Y.Extern* ; Giabbai, B.Extern* ; Demitri, N.Extern* ; Jochmans, D.Extern* ; Jonghe, S. D.Extern* ; Rymenants, J.Extern* ; Summa, V. ; Tramontano, E.Extern* ; Beccari, A. R.Extern* ; Leyssen, P.Extern* ; Storici, P.Extern* ; Neyts, J.Extern* ; Gribbon, P.Extern* ; Zaliani, A.Extern*
Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen
ACS pharmacology & translational science 4(3), 1096 - 1110 (2021) [10.1021/acsptsci.0c00216]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Korn, P.Extern* ; Classen, A.Extern* ; Murthy, S.Extern* ; Guareschi, R. ; Maksimainen, M. M.Extern* ; Lippok, B. E.Extern* ; Galera-Prat, A.Extern* ; Sowa, S. T.Extern* ; Voigt, C.Extern* ; Rossetti, G.FZJ* ; Lehtiö, L.Extern* ; Bolm, C.Extern* ; Lüscher, B. (Corresponding author)Extern*
Evaluation of 3‐ and 4‐Phenoxybenzamides as Selective Inhibitors of the Mono‐ADP‐Ribosyltransferase PARP10
ChemistryOpen 10(10), 939 - 948 (2021) [10.1002/open.202100087]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Giannos, T.Extern* ; Lešnik, S.Extern* ; Bren, U.Extern* ; Hodošček, M.Extern* ; Domratcheva, T.Extern* ; Bondar, A.-N. (Corresponding author)FZJ*
CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs
Journal of chemical information and modeling 61(8), 3964 - 3977 (2021) [10.1021/acs.jcim.1c00667]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Domínguez-Mendoza, E. A. ; Galván-Ciprés, Y. ; Martínez-Miranda, J. ; Miranda-González, C. ; Colín-Lozano, B. ; Hernández-Núñez, E.Extern* ; Hernández-Bolio, G. I.Extern* ; Palomino-Hernández, O.FZJ* ; Navarrete-Vazquez, G. (Corresponding author)Extern*
Design, Synthesis, and In Silico Multitarget Pharmacological Simulations of Acid Bioisosteres with a Validated In Vivo Antihyperglycemic Effect
Molecules 26(4), 799 - (2021) [10.3390/molecules26040799]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L.FZJ* ; Gori, M.Extern* ; Pettini, M. (Corresponding author)Extern*
Topology and Phase Transitions: A First Analytical Step towards the Definition of Sufficient Conditions
Entropy 23(11), 1414 - (2021) [10.3390/e23111414]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L.FZJ* ; Gori, M.Extern* ; Pettini, G.Extern* ; Pettini, M. (Corresponding author)Extern*
Hamiltonian chaos and differential geometry of configuration space–time
Physica / D 422, 132909 - (2021) [10.1016/j.physd.2021.132909]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Berdnikova, D. V.Extern* ; Carloni, P.FZJ* ; Krauß, S. (Corresponding author)Extern* ; Rossetti, G. (Corresponding author)FZJ*
Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding
Molecules 26(11), 3384 - (2021) [10.3390/molecules26113384]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ansari, N.Extern* ; Rizzi, V.Extern* ; Carloni, P.FZJ* ; Parrinello, M. (Corresponding author)Extern*
Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution
Journal of the American Chemical Society 143(33), 12930 - 12934 (2021) [10.1021/jacs.1c05301]2021 Files BibTeX | EndNote: XML, Text | RIS

Poster (After Call) de Bruyn, E. (Corresponding author)FZJ*RWTH* ; Zimmermann, O.FZJ* ; Grohe, M.RWTH* ; Rossetti, G.FZJ*RWTH*
Modelling Ion-Residue Interaction in Implicit Solvation for Intrinsically Disordered Proteins
2021INM & IBI Retreat 2021, RWTH AachenJülich, RWTH Aachen, Germany, 5 Oct 2021 - 6 Oct 20212021-10-052021-10-06 Fulltext BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Winkler, R. G.FZJ* ; Naegele, G.FZJ*
Quasi-two-dimensional diffusion of interacting protein monomers and dimers: A MPC simulation study
202111th LIQUID MATTER CONFERENCE 2020/2021, Prague/OnlinePrague/Online, Czech Republic, 19 Jul 2021 - 23 Jul 20212021-07-192021-07-23 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Nin-Hill, A. ; Mueller, N. P. F.FZJ* ; Molteni, C. ; Rovira, C. ; Alfonso-Prieto, M. (Corresponding author)FZJ*
Photopharmacology of Ion Channels through the Light of the Computational Microscope
International journal of molecular sciences 22(21), 12072 - (2021) [10.3390/ijms222112072] special issue: "Light-Controlled Modulation and Analysis of Neuronal Functions"2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Costanzi, E. ; Kuzikov, M. ; Esposito, F. ; Albani, S.FZJ* ; Demitri, N. ; Giabbai, B. ; Camasta, M. ; Tramontano, E. ; Rossetti, G. (Corresponding author)FZJ* ; Zaliani, A. ; Storici, P. (Corresponding author)
Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L
International journal of molecular sciences 22(21), 11779 - (2021) [10.3390/ijms222111779]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G. (Corresponding author)FZJ* ; Capelli, R.FZJ* ; Li, J. ; Carloni, P.FZJ* ; Zhao, Q.FZJ*
An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADPribosylationhydrolases inhibitors
Journal of chemical theory and computation 17(12), 7899–7911 (2021) [10.1021/acs.jctc.1c00649]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L. (Corresponding author)FZJ* ; Stamm, B. (Corresponding author)RWTH* ; Calandrini, V. (Corresponding author)FZJ*
Subdiffusive-Brownian crossover in membrane proteins: a Generalized Langevin Equation-based approach
Biophysical journal 120(21), 4722-4737 (2021) [10.1016/j.bpj.2021.09.033]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Parrinello, M. (Corresponding author) ; Rizzi, A.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials
The journal of physical chemistry letters 12(39), 9449–9454 (2021) [10.1021/acs.jpclett.1c02135]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Nägele, G.FZJ* ; Winkler, R. G.FZJ*
Hydrodynamics of immiscible binary fluids with viscosity contrast: a multiparticle collision dynamics approach
Soft matter 17(34), 7978 - 7990 (2021) [10.1039/D1SM00541C]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zuo, K. ; Marjault, H.-B. ; Bren, K. L. ; Rossetti, G.FZJ* ; Nechushtai, R. ; Carloni, P. (Corresponding author)FZJ*
The two redox states of the human NEET proteins’ [2Fe–2S] clusters
Journal of biological inorganic chemistry 26, 763–774 (2021) [10.1007/s00775-021-01890-8]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M. (Corresponding author)FZJ*
Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose
The journal of membrane biology 254(4), 343-352 (2021) [10.1007/s00232-021-00182-1]2021 Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Chiariello, M. G. (Corresponding author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Ippoliti, E.FZJ* ; Fahlke, C. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ*
Mechanisms Underlying Proton Release in CLC-type F – /H + Antiporters
The journal of physical chemistry letters 12(18), 4415 - 4420 (2021) [10.1021/acs.jpclett.1c00361]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bolnykh, V.FZJ* ; Rossetti, G.FZJ* ; Rothlisberger, U. ; Carloni, P. (Corresponding author)FZJ*
Expanding the boundaries of ligand–target modeling by exascale calculations
Wiley interdisciplinary reviews / Computational Molecular Science 11(4), e1535 (2021) [10.1002/wcms.1535]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Korshunova, K.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme
The journal of physical chemistry <Washington, DC> / B 125(3), 789 - 797 (2021) [10.1021/acs.jpcb.0c09805]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article D'Arrigo, G. ; Gianquinto, E. ; Rossetti, G. (Corresponding author)FZJ* ; Cruciani, G. ; Lorenzetti, S. ; Spyrakis, F.
Binding of Androgen- and Estrogen-Like Flavonoids to Their Cognate (Non)Nuclear Receptors: A Comparison by Computational Prediction
Molecules 26(6), 1613 - (2021) [10.3390/molecules26061613]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Gossen, J.FZJ* ; Albani, S.FZJ* ; Hanke, A.Extern* ; Joseph, B. P.FZJ* ; Bergh, C.Extern* ; Kuzikov, M.Extern* ; Costanzi, E. ; Manelfi, C. ; Storici, P. ; Gribbon, P. ; Beccari, A. R. ; Talarico, C.Extern* ; Spyrakis, F.Extern* ; Lindahl, E.Extern* ; Zaliani, A.Extern* ; Carloni, P.FZJ* ; Wade, R. C.Extern* ; Musiani, F.Extern* ; Kokh, D. B.Extern* ; Rossetti, G. (Corresponding author)FZJ*
A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics
ACS pharmacology & translational science 4(3), 1079–1095 (2021) [10.1021/acsptsci.0c00215]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schmitz-Hübsch, T. (Corresponding author) ; Lux, S. ; Bauer, P. ; Brandt, A. U. ; Schlapakow, E. ; Greschus, S. ; Scheel, M. ; Gärtner, H. ; Kirlangic, M. E. ; Gras, V. ; Timmann, D. ; Synofzik, M. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Shah, N. J.FZJ* ; Schöls, L. ; Kopp, U. ; Bußenius, L. ; Oberwahrenbrock, T. ; Zimmermann, H. ; Pfueller, C. ; Kadas, E. M. ; Rönnefarth, M. ; Grosch, A. S. ; Endres, M. ; Amunts, K.FZJ* ; Friedemann, P. ; Doss, S. ; Minnerop, M. (Corresponding author)FZJ*
Spinocerebellar ataxia type 14: Refining clinico-genetic diagnosis in a rare adult-onset disorder
Annals of Clinical and Translational Neurology 8(4), 774-789 (2021) [10.1002/acn3.51315]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lai, H. T. T. ; Giorgetti, A.FZJ* ; Rossetti, G.FZJ* ; Nguyen, T. T. ; Carloni, P.FZJ* ; Kranjc Pietrucci, A. (Corresponding author)FZJ*
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations
Molecules 26(5), 1250 - (2021) [10.3390/molecules26051250]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Manelfi, C. ; Gossen, J.FZJ* ; Gervasoni, S. ; Talarico, C. ; Albani, S.FZJ* ; Philipp, B. J. ; Musiani, F. ; Vistoli, G. ; Rossetti, G.FZJ* ; Beccari, A. R. ; Pedretti, A. (Corresponding author)
Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease
Molecules 26(4), 797 - (2021) [10.3390/molecules26040797]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sitani, D. (Corresponding author)FZJ* ; Giorgetti, A.FZJ* ; Alfonso‐Prieto, M.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Robust Principal Component Analysis‐based Prediction of Protein‐Protein Interaction Hot spots ( RBHS )
Proteins 89(6), 639-647 (2021) [10.1002/prot.26047]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ferraro, M. ; Moroni, E. ; Ippoliti, E.FZJ* ; Rinaldi, S. ; Sanchez-Martin, C. ; Rasola, A. ; Pavarino, L. F. (Corresponding author) ; Colombo, G. (Corresponding author)
Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1
The journal of physical chemistry <Washington, DC> / B 125(1), 101 - 114 (2021) [10.1021/acs.jpcb.0c09742]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maleeva, G. (Corresponding author) ; Nin-Hill, A. ; Rustler, K. ; Petukhova, E. ; Ponomareva, D. ; Mukhametova, E. ; Gomila-Juaneda, A. ; Wutz, D. ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; König, B. ; Gorostiza, P. ; Bregestovski, P. (Corresponding author)
Subunit-specific photocontrol of glycine receptors by azobenzene-nitrazepam photoswitcher
eNeuro 8(1), ENEURO.0294-20.2020 (2021) [10.1523/ENEURO.0294-20.2020]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kanellopoulos, A. K. ; Mariano, V. ; Spinazzi, M. ; Woo, Y. J. ; McLean, C. ; Pech, U. ; Li, K. W. ; Armstrong, J. D.FZJ* ; Giangrande, A. ; Callaerts, P. ; Smit, A. B. ; Abrahams, B. S. ; Fiala, A. ; Achsel, T. ; Bagni, C. (Corresponding author)
Aralar Sequesters GABA into Hyperactive Mitochondria, Causing Social Behavior Deficits
Cell 180(6), 1178 - 1197.e20 (2020) [10.1016/j.cell.2020.02.044]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Guaitoli, V. ; Alvarez-Ginarte, Y. M. ; Montero-Cabrera, L. A. (Corresponding author) ; Bencomo-Martínez, A. ; Badel, Y. P. ; Giorgetti, A.FZJ* ; Suku, E.
A computational strategy to understand structure-activity relationship of 1,3-disubstituted imidazole [1,5-α] pyrazine derivatives described as ATP competitive inhibitors of the IGF-1 receptor related to Ewing sarcoma
Journal of molecular modeling 26(8), 222 (2020) [10.1007/s00894-020-04470-w]2020 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Marchetto, A.FZJ* ; Si Chaib, Z.FZJ* ; Rossi, C. A. ; Ribeiro, R.FZJ* ; Pantano, S. ; Rossetti, G. (Corresponding author)FZJ* ; Giorgetti, A. (Corresponding author)FZJ*
CGMD Platform: Integrated Web Servers for the Preparation, Running, and Analysis of Coarse-Grained Molecular Dynamics Simulations
Molecules 25(24), 5934 - (2020) [10.3390/molecules25245934]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ritacco, I. ; Saltalamacchia, A. ; Spinello, A. ; Ippoliti, E.FZJ* ; Magistrato, A. (Corresponding author)
All-Atom Simulations Disclose How Cytochrome Reductase Reshapes the Substrate Access/Egress Routes of Its Partner CYP450s
The journal of physical chemistry letters 11(4), 1189 - 1193 (2020) [10.1021/acs.jpclett.9b03798]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bolnykh, V. (Corresponding author)FZJ* ; Olsen, J. M. H. (Corresponding author) ; Meloni, S. ; Bircher, M. P. ; Ippoliti, E.FZJ* ; Carloni, P.FZJ* ; Rothlisberger, U. (Corresponding author)
MiMiC: Multiscale Modeling in Computational Chemistry
Frontiers in molecular biosciences 7, 45 (2020) [10.3389/fmolb.2020.00045]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Gomila, A. M. J.Extern* ; Rustler, K. ; Maleeva, G. ; Nin-Hill, A. ; Wutz, D. ; Bautista-Barrufet, A. ; Rovira, X.Extern* ; Bosch, M.Extern* ; Mukhametova, E. ; Petukhova, E. ; Ponomareva, D. ; Mukhamedyarov, M. ; Peiretti, F. ; Alfonso-Prieto, M.FZJ* ; Rovira, C. (Corresponding author)Extern* ; König, B. (Corresponding author)Extern* ; Bregestovski, P. (Corresponding author)Extern* ; Gorostiza, P. (Corresponding author)Extern*
Photocontrol of Endogenous Glycine Receptors In Vivo
Cell chemical biology 27(11), 1425 - 1433.e7 (2020) [10.1016/j.chembiol.2020.08.005]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Preprint Toledo, M. A. S. ; Gatz, M. ; Sontag, S. ; Gleixner, K. V. ; Eisenwort, G. ; Feldberg, K. ; Kluge, F. ; Guareschi, R.FZJ* ; Rossetti, G.FZJ* ; Sechi, A. S. ; Dufva, O. M. J. ; Mustjoki, S. M. ; Maurer, A. ; Schüler, H. M. ; Goetzke, R. ; Braunschweig, T. ; Simonowski, A. ; Panse, J. ; Jawhar, M. ; Reiter, A. ; Hilberg, F. ; Ettmayer, P. ; Wagner, W. ; Koschmieder, S. ; Brümmendorf, T. H. ; Valent, P. ; Chatain, N. ; Zenke, M. (Corresponding author)
Nintedanib Targets KIT D816V Neoplastic Cells Derived from Induced Pluripotent Stem cells of Systemic Mastocytosis
[10.1101/2020.05.06.080150] Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Altenburg, B. ; Frings, M. ; Schöbel, J.-H. ; Goßen, J. ; Pannen, K. ; Vanderliek, K. ; Rossetti, G.FZJ* ; Koschmieder, S. ; Chatain, N. ; Bolm, C. (Corresponding author)
Chiral Analogues of PFI-1 as BET Inhibitors and Their Functional Role in Myeloid Malignancies
ACS medicinal chemistry letters 11(10), 1928–1934 (2020) [10.1021/acsmedchemlett.9b00625]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Si Chaib, Z.FZJ* ; Marchetto, A.FZJ* ; Dishnica, K. ; Carloni, P.FZJ* ; Giorgetti, A.FZJ* ; Rossetti, G. (Corresponding author)FZJ*
Impact of Cholesterol on the Stability of Monomeric and Dimeric Forms of the Translocator Protein TSPO: A Molecular Simulation Study
Molecules 25(18), 4299 - (2020) [10.3390/molecules25184299]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schneider, J.FZJ* ; Ribeiro, R. ; Alfonso-Prieto, M.FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Giorgetti, A. (Corresponding author)FZJ*
Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes
Frontiers in molecular biosciences 7, 576689 (2020) [10.3389/fmolb.2020.576689]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Preprint Schmitz-Hübsch, T. (Corresponding author) ; Lux, S. ; Bauer, P. ; Schlapakow, E. ; Greschus, S. ; Scheel, M. ; Gärtner, H. ; Kirlangic, M. E. ; Gras, V. ; Timmann, D. ; Synofzik, M. ; Giorgetti, A. ; Carloni, P.FZJ* ; Shah, N. J.FZJ* ; Schöls, L. ; Kopp, U. ; Bussenius, L. ; Oberwahrenbrock, T. ; Zimmermann, H. ; Pfueller, C. ; Kadas, E. M. ; Rönnefarth, M. ; Grosch, A. S. ; Endres, M. ; Amunts, K.FZJ* ; Friedemann, P. ; Doss, S. ; Minnerop, M.FZJ*
Spinocerebellar ataxia type 14: refining clinico-genetic diagnosis in a rare adult-onset disorder
Annals of Clinical and Translational Neurology (2020)2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Invited) Alfonso-Prieto, M. (Corresponding author)FZJ* ; Giorgetti, A.FZJ* ; Carloni, P.FZJ*
S14- A computational view on coffee perception: modeling and simulations of chemosensory receptors
2020XXIXth Annual Meeting of the European Chemoreception Research Organization, ECRO 2019, TriesteTrieste, Italy, 11 Sep 2019 - 14 Sep 20192019-09-112019-09-14 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Bolnykh, V. (Corresponding author)FZJ* ; Rothlisberger, U. ; Carloni, P.FZJ*
Biomolecular Simulation: A Perspective from High Performance Computing
Israel journal of chemistry 60(7), 694 - 704 (2020) [10.1002/ijch.202000022]2020 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R. (Corresponding author)FZJ* ; Lyu, W.FZJ* ; Bolnykh, V.FZJ* ; Meloni, S.Extern* ; Olsen, J. M. H.Extern* ; Rothlisberger, U.Extern* ; Parrinello, M.Extern* ; Carloni, P.FZJ*
Accuracy of Molecular Simulation-Based Predictions of k off Values: A Metadynamics Study
The journal of physical chemistry letters 11(15), 6373 - 6381 (2020) [10.1021/acs.jpclett.0c00999]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Barroso da Silva, F. L. (Corresponding author) ; Carloni, P.FZJ* ; Cheung, D. ; Cottone, G. ; Donnini, S. ; Foegeding, E. A. ; Gulzar, M. ; Jacquier, J. C. ; Lobaskin, V. ; MacKernan, D. ; Mohammad Hosseini Naveh, Z. ; Radhakrishnan, R. ; Santiso, E. E.
Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations
Annual review of food science and technology 11(1), 365-387 (2020) [10.1146/annurev-food-032519-051640]2020 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Nechushtai, R. ; Karmi, O. ; Zuo, K.RWTH* ; Marjault, H.-B. ; Darash-Yahana, M. ; Sohn, Y.-S. ; King, S. D. ; Zandalinas, S. I. ; Carloni, P.FZJ* ; Mittler, R. (Corresponding author)
The balancing act of NEET proteins: Iron, ROS, calcium and metabolism
Biochimica et biophysica acta / Molecular cell research Molecular cell research 1867(11), 118805 - (2020) [10.1016/j.bbamcr.2020.118805]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Chiariello, M. G. (Corresponding author)FZJ* ; Bolnykh, V.FZJ* ; Ippoliti, E.FZJ* ; Meloni, S. ; Olsen, J. M. H.Extern* ; Beck, T. ; Rothlisberger, U.Extern* ; Fahlke, C. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ*
Molecular Basis of CLC Antiporter Inhibition by Fluoride
Journal of the American Chemical Society 142(16), 7254 - 7258 (2020) [10.1021/jacs.9b13588]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zaccagnini, L. ; Rossetti, G.FZJ* ; Tran, T. H. ; Salzano, G. ; Gandini, A. ; Colini Baldeschi, A. ; Bolognesi, M. L. ; Carloni, P.FZJ* ; Legname, G. (Corresponding author)
In silico/in vitro screening and hit evaluation identified new phenothiazine anti-prion derivatives
European journal of medicinal chemistry 196, 112295 (2020) [10.1016/j.ejmech.2020.112295]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schneider, J. (Corresponding author)FZJ* ; Korshunova, K.FZJ* ; Si Chaib, Z.FZJ* ; Giorgetti, A.FZJ* ; Alfonso-Prieto, M.FZJ* ; Carloni, P.FZJ*
Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-based Hybrid Molecular Mechanics/Coarse-Grained Approach
Journal of chemical information and modeling 60(10), 5103–5116 (2020) [10.1021/acs.jcim.0c00661]2020 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Palomino, O.FZJ* ; Buratti, F. A. ; Sacco, P. S. ; Rossetti, G.FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Fernandez, C. O. (Corresponding author)
Role of Tyr-39 for the Structural Features of α-Synuclein and for the Interaction with a Strong Modulator of Its Amyloid Assembly
International journal of molecular sciences 21(14), 5061 - (2020) [10.3390/ijms21145061]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Palomino, O.FZJ* ; Margreiter, M. A.FZJ* ; Rossetti, G. (Corresponding author)FZJ*
Challenges in RNA Regulation in Huntington's Disease: Insights from Computational Studies
Israel journal of chemistry 60(7), 681-693 (2020) [10.1002/ijch.202000021]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Baldessari, F. ; Capelli, R. (Corresponding author)FZJ* ; Carloni, P.FZJ* ; Giorgetti, A.FZJ*
Coevolutionary Data-based Interaction Networks Approach Highlighting Key Residues across Protein Families: the Case of the G-protein Coupled Receptors
Computational and structural biotechnology journal 18, 1153-1159 (2020) [10.1016/j.csbj.2020.05.003]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Preprint Maggi, L. (Corresponding author)FZJ*RWTH* ; Carloni, P.FZJ*RWTH* ; Rossetti, G.FZJ*RWTH*
Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960
Scientific reports (2020)2020 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Maggi, L. (Corresponding author)FZJ* ; Carloni, P.FZJ* ; Rossetti, G.FZJ*
Modeling the allosteric modulation on a G-Protein Coupled Receptor: the case of M2 muscarinic Acetylcholine Receptor in complex with LY211960
Scientific reports 10(1), 3037 (2020) [10.1038/s41598-020-59289-5]2020 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ritacco, I. ; Spinello, A. ; Ippoliti, E.FZJ* ; Magistrato, A. (Corresponding author)
Post-Translational Regulation of CYP450s Metabolism As Revealed by All-Atoms Simulations of the Aromatase Enzyme
Journal of chemical information and modeling 59(6), 2930 - 2940 (2019) [10.1021/acs.jcim.9b00157]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bolnykh, V. (Corresponding author)FZJ* ; Olsen, J. M. H. (Corresponding author)Extern* ; Meloni, S.Extern* ; Bircher, M. P.Extern* ; Ippoliti, E.FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Rothlisberger, U. (Corresponding author)Extern*
Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC
Journal of chemical theory and computation 15(10), 5601 - 5613 (2019) [10.1021/acs.jctc.9b00424]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bruce, N. J. ; Narzi, D. ; Trpevski, D. ; van Keulen, S. C. ; Nair, A. G. ; Röthlisberger, U. ; Wade, R. C. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ* ; Hellgren Kotaleski, J. (Corresponding author)
Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals
PLoS Computational Biology 15(10), e1007382 - (2019) [10.1371/journal.pcbi.1007382]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G.FZJ* ; Kless, A. ; Lai, L. ; Outeiro, T. F. ; Carloni, P. (Corresponding author)FZJ*
Investigating targets for neuropharmacological intervention by molecular dynamics simulations
Biochemical Society transactions 47(3), 909 - 918 (2019) [10.1042/BST20190048]2019 BibTeX | EndNote: XML, Text | RIS

Journal Article Wirthschaft, P. ; Bode, J. ; Soni, H. ; Dietrich, F. ; Krüwel, T. ; Fischer, B. ; Knobbe-Thomsen, C. B. ; Rossetti, G.FZJ* ; Hentschel, A. ; Mack, N. ; Schönig, K. ; Breckwoldt, M. O. ; Schmandke, A. ; Pusch, S. ; Medenbach, J. ; Bendszus, M. ; Schwab, M. E. ; von Deimling, A. ; Kool, M. ; Herold-Mende, C. ; Reifenberger, G. ; Ahrends, R. ; Tews, B. (Corresponding author)
RhoA regulates translation of the Nogo-A decoy SPARC in white matter-invading glioblastomas
Acta neuropathologica 138(2), 275 - 293 (2019) [10.1007/s00401-019-02021-z]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rehman, M. ; Vodret, S. ; Braga, L. ; Guarnaccia, C. ; Celsi, F. ; Rossetti, G.FZJ* ; Martinelli, V. ; Battini, T. ; Long, C. ; Vukusic, K. ; Kocijan, T. ; Collesi, C. ; Ring, N. ; Skoko, N. ; Giacca, M. ; Del Sal, G. ; Confalonieri, M. ; Raspa, M. ; Marcello, A. ; Myers, M. P. ; Crovella, S. ; Carloni, P.FZJ* ; Zacchigna, S. (Corresponding author)
High-throughput screening discovers antifibrotic properties of haloperidol by hindering myofibroblast activation
JCI insight 4(8), e123987 (2019) [10.1172/jci.insight.123987]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R. (Corresponding author)FZJ* ; Carloni, P.FZJ* ; Parrinello, M.
Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics
The journal of physical chemistry letters 10(12), 3495 - 3499 (2019) [10.1021/acs.jpclett.9b01183]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R. (Corresponding author)FZJ* ; Bochicchio, A. ; Piccini, G. ; Casasnovas, R. ; Carloni, P. (Corresponding author)FZJ* ; Parrinello, M.
Chasing the Full Free Energy Landscape of Neuroreceptor/Ligand Unbinding by Metadynamics Simulations
Journal of chemical theory and computation 15(5), 3354 - 3361 (2019) [10.1021/acs.jctc.9b00118]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R. (Corresponding author)FZJ* ; Carloni, P.FZJ* ; Camilloni, C. ; Bonomi, M. ; Tribello, G. ; Bussi, G.
Promoting transparency and reproducibility in enhanced molecular simulations
Nature methods 16(8), 670 - 673 (2019) [10.1038/s41592-019-0506-8]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maleeva, G.AMU* ; Wutz, D. ; Rustler, K. ; Nin‐Hill, A. ; Petukhova, E. ; Bautista‐Barrufet, A. ; Gomila‐Juaneda, A. ; Scholze, P. ; Peiretti, F.AMU* ; Rovira, C. ; König, B. ; Gorostiza, P. (Corresponding author) ; Bregestovski, P. (Corresponding author)AMU* ; Alfonso-Prieto, M. (Corresponding author)FZJ*
A photoswitchable GABA receptor channel blocker
British journal of pharmacology 176(15), 2661-2677 (2019) [10.1111/bph.14689]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Olsen, J. M. H. (Corresponding author) ; Bolnykh, V.FZJ* ; Meloni, S. ; Ippoliti, E.FZJ* ; Bircher, M. P. ; Carloni, P.FZJ* ; Rothlisberger, U.
MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
Journal of chemical theory and computation 15(6), 3810 - 3823 (2019) [10.1021/acs.jctc.9b00093]2019 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Fierro, F.FZJ* ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Meyerhof, W. ; Alfonso-Prieto, M. (Corresponding author)FZJ*
Dual binding mode of “bitter sugars” to their human bitter taste receptor target
Scientific reports 9(1), 8437 (2019) [10.1038/s41598-019-44805-z]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kotredes, K. P. ; Razmpour, R. ; Lutton, E. ; Alfonso-Prieto, M.FZJ* ; Ramirez, S. H. ; Gamero, A. M. (Corresponding author)
Characterization of cancer-associated IDH2 mutations that differ in tumorigenicity, chemosensitivity and 2-hydroxyglutarate production
OncoTarget 10(28), 2675-2692 (2019) [10.18632/oncotarget.26848]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M.FZJ* ; Navarini, L. ; Carloni, P. (Corresponding author)FZJ*
Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations
Frontiers in molecular biosciences 6, 29 (2019) [10.3389/fmolb.2019.00029]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M.FZJ* ; Giorgetti, A.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Multiscale simulations on human Frizzled and Taste2 GPCRs
Current opinion in structural biology 55, 8-16 (2019) [10.1016/j.sbi.2019.02.009]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Amundarain, M. J. ; Viso, J. F. ; Zamarreño, F. ; Giorgetti, A. (Corresponding author)FZJ* ; Costabel, M. (Corresponding author)
Orthosteric and benzodiazepine cavities of the α 1 β 2 γ 2 GABA A receptor: insights from experimentally validated in silico methods
Journal of biomolecular structure & dynamics 37(6), 1597 - 1615 (2019) [10.1080/07391102.2018.1462733]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Amundarain, M. J. ; Ribeiro, R. P. ; Costabel, M. D. ; Giorgetti, A. (Corresponding author)FZJ*
GABA A receptor family: overview on structural characterization
Future medicinal chemistry 11(3), 229 - 245 (2019) [10.4155/fmc-2018-0336]2019 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Tarenzi, T.FZJ* ; Calandrini, V. (Corresponding author)FZJ* ; Potestio, R. (Corresponding author) ; Carloni, P.FZJ*
Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor–Ligand Complexes
Journal of chemical theory and computation 15(3), 2101–2109 (2019) [10.1021/acs.jctc.9b00040]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sánchez-López, C. ; Rossetti, G.FZJ* ; Quintanar, L. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Structural Determinants of the Prion Protein N-Terminus and Its Adducts with Copper Ions
International journal of molecular sciences 20(1), 18 (2019) [10.3390/ijms20010018]2019 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Pietropaolo, A. (Corresponding author) ; Magrì, A. ; Greco, V. ; Losasso, V. ; La Mendola, D. (Corresponding author) ; Sciuto, S. ; Carloni, P.FZJ* ; Rizzarelli, E.
Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays
ACS chemical neuroscience 9(5), 1095 - 1103 (2018) [10.1021/acschemneuro.7b00470]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Capaldi, S. ; Suku, E. ; Antolini, M. ; Di Giacobbe, M. ; Giorgetti, A. (Corresponding author)FZJ* ; Buffelli, M.
Allosteric sodium binding cavity in GPR3: a novel player in modulation of Aβ production
Scientific reports 8(1), 11102 (2018) [10.1038/s41598-018-29475-7]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R. (Corresponding author)FZJ* ; Caracciolo, S. (Corresponding author) ; Di Gioacchino, A. (Corresponding author) ; Malatesta, E. M. (Corresponding author)
Exact value for the average optimal cost of the bipartite traveling salesman and two-factor problems in two dimensions
Physical review / E 98(3), 030101 (2018) [10.1103/PhysRevE.98.030101]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Capelli, R.FZJ* ; Peri, C. ; Villa, R. ; Nithichanon, A. ; Conchillo-Solé, O. ; Yero, D. ; Gagni, P. ; Chiari, M. ; Lertmemongkolchai, G. ; Cretich, M. ; Daura, X. ; Bolognesi, M. ; Colombo, G. (Corresponding author) ; Gourlay, L. J. (Corresponding author)
BPSL1626: Reverse and Structural Vaccinology Reveal a Novel Candidate for Vaccine Design Against Burkholderia pseudomallei
Antibodies 7(3), 26 - (2018) [10.3390/antib7030026]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lyu, , Wenping ; Arnesano, F. ; Carloni, P. (Corresponding author)FZJ* ; Natile, G. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ*
Effect of in vivo post-translational modifications of the HMGB1 protein upon binding to platinated DNA: a molecular simulation study
Nucleic acids symposium series 46(22), 11687 - 11697 (2018) [10.1093/nar/gky1082]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bochicchio, A. (Corresponding author)FZJ* ; Krepl, M. (Corresponding author) ; Yang, F. ; Varani, G. ; Sponer, J. ; Carloni, P. (Corresponding author)FZJ*
Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study
PLoS Computational Biology 14(12), e1006642 - (2018) [10.1371/journal.pcbi.1006642]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Reiners, M. ; Margreiter, M. A. ; Oslender-Bujotzek, A. ; Rossetti, G.FZJ* ; Gründer, S. (Corresponding author) ; Schmidt, A. (Corresponding author)
The Conorfamide RPRFa Stabilizes the Open Conformation of Acid-Sensing Ion Channel 3 via the Nonproton Ligand–Sensing Domain
Molecular pharmacology 94(4), 1114 - 1124 (2018) [10.1124/mol.118.112375]2018 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Chang, P. (Editor) ; Bütepage, M. (Corresponding author) ; Krieg, S. ; Eckei, L. ; Li, J. ; Rossetti, G.FZJ* ; Verheugd, P. ; Lüscher, B. (Corresponding author)
Assessment of Intracellular Auto-Modification Levels of ARTD10 Using Mono-ADP-Ribose-Specific Macrodomains 2 and 3 of Murine Artd8
2018ADP-ribosylation and NAD+ Utilizing Enzymes / Chang, Paul (Editor) ; New York, NY : Springer New York, 2018, Chapter 4 ; ISSN: 1064-3745=1940-6029 ; ISBN: 978-1-4939-8587-6=978-1-4939-8588-3 ; doi:10.1007/978-1-4939-8588-3 New York, NY : Springer New York, Methods in Molecular Biology 1813, 41 - 63 (2018) [10.1007/978-1-4939-8588-3_4]2018 BibTeX | EndNote: XML, Text | RIS

Journal Article Matthes, F.FZJ* ; Massari, S. ; Bochicchio, A.FZJ* ; Schorpp, K. ; Schilling, J. ; Weber, S. ; Offermann, N. ; Desantis, J. ; Wanker, E. ; Carloni, P.FZJ* ; Hadian, K. ; Tabarrini, O. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ* ; Krauss, S. (Corresponding author)
Reducing Mutant Huntingtin Protein Expression in Living Cells by a Newly Identified RNA CAG Binder
ACS chemical neuroscience 9(6), 1399 - 1408 (2018) [10.1021/acschemneuro.8b00027]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bütepage, M. ; Preisinger, C. ; von Kriegsheim, A. ; Scheufen, A. ; Lausberg, E. ; Li, J. ; Kappes, F. ; Feederle, R. ; Ernst, S. ; Eckei, L. ; Krieg, S. ; Müller-Newen, G. ; Rossetti, G.FZJ* ; Feijs, K. L. H. ; Verheugd, P. ; Lüscher, B. (Corresponding author)
Nucleolar-nucleoplasmic shuttling of TARG1 and its control by DNA damage-induced poly-ADP-ribosylation and by nucleolar transcription
Scientific reports 8(1), 6748 (2018) [10.1038/s41598-018-25137-w]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maggi, L.FZJ* ; Carloni, P.FZJ* ; Rossetti, G. (Corresponding author)FZJ*
Vibrational Energy in Proteins Correlates with Topology
The journal of physical chemistry letters 9(22), 6393 - 6398 (2018) [10.1021/acs.jpclett.8b02380]2018 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Cao, R.FZJ* ; Giorgetti, A.FZJ* ; Bauer, A.FZJ* ; Neumaier, B.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Carloni, P.FZJ*
Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study
Molecules 23(10), 2616 - (2018) [10.3390/molecules23102616]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zeng, J.FZJ* ; Guareschi, R.FZJ* ; Damre, M. ; Cao, R. ; Kless, A. ; Neumaier, B.FZJ* ; Bauer, A.FZJ* ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Rossetti, G. (Corresponding author)FZJ*
Structural Prediction of the Dimeric Form of the Mammalian Translocator Membrane Protein TSPO: A Key Target for Brain Diagnostics
International journal of molecular sciences 19(9), 2588 - (2018) [10.3390/ijms19092588]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schneider, J.FZJ*RWTH* ; Korshunova, K.FZJ*RWTH* ; Musiani, F.Extern* ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; Giorgetti, A.FZJ* ; Carloni, P. (Corresponding author)FZJ*RWTH*
Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations
Biochemical and biophysical research communications 498(2), 366 - 374 (2018) [10.1016/j.bbrc.2018.01.160] special issue: "Multiscale Modeling"2018 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Nguyen, T. H. ; Zhang, C. (Corresponding author)FZJ* ; Weichselbaum, E. ; Knyazev, D. G. ; Pohl, P. ; Carloni, P. (Corresponding author)FZJ*
Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion
PLoS one 13(2), e0193454 - (2018) [10.1371/journal.pone.0193454]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Genna, V. ; Carloni, P.FZJ* ; De Vivo, M. (Corresponding author)FZJ*
A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases
Journal of the American Chemical Society 140(9), 3312 - 3321 (2018) [10.1021/jacs.7b12446]2018 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Franco-Ulloa, S. ; La Sala, G. ; Miscione, G. (Corresponding author) ; De Vivo, M. (Corresponding author)FZJ*
Novel Bacterial Topoisomerase Inhibitors Exploit Asp83 and the Intrinsic Flexibility of the DNA Gyrase Binding Site
International journal of molecular sciences 19(2), 453 - (2018) [10.3390/ijms19020453]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Karmi, O. ; Marjault, H.-B. ; Pesce, L.FZJ* ; Carloni, P.FZJ* ; Onuchic, J. N. ; Jennings, P. A. ; Mittler, R. ; Nechushtai, R. (Corresponding author)
The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease
Journal of biological inorganic chemistry 23(4), 599-612 (2018) [10.1007/s00775-018-1538-8]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Genna, V. ; Colombo, M. ; De Vivo, M. (Corresponding author)FZJ* ; Marcia, M. (Corresponding author)
Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes
Structure 26, 40-50 (2018) [10.1016/j.str.2017.11.008]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ortega, J. A. ; Riccardi, L. ; Minniti, E. ; Borgogno, M. ; Arencibia, J. M. ; Greco, M. L. ; Minarini, A. ; Sissi, C. (Corresponding author) ; De Vivo, M. (Corresponding author)FZJ*
Pharmacophore Hybridization To Discover Novel Topoisomerase II Poisons with Promising Antiproliferative Activity
Journal of medicinal chemistry 61(3), 1375-1379 (2018) [10.1021/acs.jmedchem.7b01388]2018 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schmidt, A. (Corresponding author) ; Rossetti, G.FZJ* ; Joussen, S. ; Gründer, S. (Corresponding author)
Diminazene Is a Slow Pore Blocker of Acid-Sensing Ion Channel 1a (ASIC1a)
Molecular pharmacology 92(6), 665 - 675 (2017) [10.1124/mol.117.110064]2017 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Martín-Santamaría, S. (Editor) ; De Vivo, M. (Corresponding author)FZJ* ; Masetti, M. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ*
Chapter 12. Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targets
2017Computational Tools for Chemical Biology / Martín-Santamaría, Sonsoles (Editor) ; Cambridge : Royal Society of Chemistry, 2017, ; ISBN: ; doi:10.1039/9781788010139 Cambridge : Royal Society of Chemistry 317 - 348 (2017) [10.1039/9781788010139-00317]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article De Vivo, M. (Corresponding author)FZJ* ; Cavalli, A. (Corresponding author)
Recent advances in dynamic docking for drug discovery
Wiley interdisciplinary reviews / Computational Molecular Science 7(6), e1320 - (2017) [10.1002/wcms.1320]2017 BibTeX | EndNote: XML, Text | RIS

Journal Article La Sala, G. ; Decherchi, S. ; De Vivo, M. (Corresponding author)FZJ* ; Rocchia, W. (Corresponding author)
Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis
ACS central science 3(9), 949 - 960 (2017) [10.1021/acscentsci.7b00211]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Minniti, E. ; Byl, J. A. W. ; Riccardi, L. ; Sissi, C. ; Rosini, M. ; De Vivo, M.FZJ* ; Minarini, A. (Corresponding author) ; Osheroff, N. (Corresponding author)
Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα
Bioorganic & medicinal chemistry letters 27(20), 4687 - 4693 (2017) [10.1016/j.bmcl.2017.09.011]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Pesce, L.FZJ* ; Calandrini, V.FZJ* ; Marjault, H.-B. ; Lipper, C. H. ; Rossetti, G.FZJ* ; Mittler, R. ; Jennings, P. A. ; Nechushtai, R. ; Carloni, P. (Corresponding author)FZJ* ; Bauer, A.FZJ*
Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release
The journal of physical chemistry <Washington, DC> / B 121(47), 10648–10656 (2017) [10.1021/acs.jpcb.7b10584]2017 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Tarenzi, T. ; Calandrini, V. (Corresponding author)FZJ* ; Potestio, R. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ*
Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme
Journal of chemical theory and computation 13(11), 5647–5657 (2017) [10.1021/acs.jctc.7b00508]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a book Rossetti, G.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Structural Modeling of Human Prion Protein's Point Mutations
2017Prion Protein / Rossetti, Giulia ; : Elsevier, 2017, ; ISSN: 18771173 ; ISBN: 9780128112267 ; doi:10.1016/bs.pmbts.2017.07.001 Amsterdam [u.a.] : Elsevier, Progress in Molecular Biology and Translational Science 150, 105 - 122 (2017) [10.1016/bs.pmbts.2017.07.001]2017 BibTeX | EndNote: XML, Text | RIS

Journal Article Fierro, F. (First author)FZJ* ; Suku, E. (First author) ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; Giorgetti, A. (Corresponding author)FZJ* ; Cichon, S.FZJ* ; Carloni, P. (Last author)FZJ*
Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis
Frontiers in molecular biosciences 4, 63 (2017) [10.3389/fmolb.2017.00063]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ortega, J. A. ; Arencibia, J. M. ; La Sala, G. ; Borgogno, M. ; Bauer, I. ; Bono, L. ; Braccia, C. ; Armirotti, A. ; Girotto, S. ; Ganesan, A. ; De Vivo, M. (Corresponding author)FZJ*
Pharmacophore Identification and Scaffold Exploration to Discover Novel, Potent, and Chemically Stable Inhibitors of Acid Ceramidase in Melanoma Cells
Journal of medicinal chemistry 60(13), 5800 - 5815 (2017) [10.1021/acs.jmedchem.7b00472]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Riccardi, L. ; Gabrielli, L. ; Sun, X. ; De Biasi, F. ; Rastrelli, F. ; Mancin, F. ; De Vivo, M. (Corresponding author)FZJ*
Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition
Chem 3(1), 92 - 109 (2017) [10.1016/j.chempr.2017.05.016]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Suku, E. ; Fierro, F.FZJ* ; Giorgetti, A. (Corresponding author)FZJ* ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; Carloni, P.FZJ*
Multi-scale simulations of membrane proteins: The case of bitter taste receptors
Journal of science 2(1), 15 - 21 (2017) [10.1016/j.jsamd.2017.03.001]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Quan, C. ; Stamm, B. (Corresponding author)FZJ*
Meshing molecular surfaces based on analytical implicit representation
Journal of molecular graphics and modelling 71, 200 - 210 (2017) [10.1016/j.jmgm.2016.11.008]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Aviat, F. ; Levitt, A. ; Stamm, B.FZJ* ; Maday, Y. ; Ren, P. ; Ponder, J. W. ; Lagardère, L. (Corresponding author) ; Piquemal, J.-P. (Corresponding author)
Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
Journal of chemical theory and computation 13(1), 180 - 190 (2017) [10.1021/acs.jctc.6b00981]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Riccardi, L. ; Arencibia, J. M. ; Bono, L. ; Armirotti, A. ; Girotto, S. ; De Vivo, M. (Corresponding author)FZJ*
Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase
Biochimica et biophysica acta / Molecular and cell biology of lipids 1862(5), 441 - 451 (2017) [10.1016/j.bbalip.2017.01.002]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Campaner, E. ; Rustighi, A. ; Zannini, A. ; Cristiani, A. ; Piazza, S. ; Ciani, Y. ; Kalid, O. ; Golan, G. ; Baloglu, E. ; Shacham, S. ; Valsasina, B. ; Cucchi, U. ; Pippione, A. C. ; Lolli, M. L. ; Giabbai, B. ; Storici, P. ; Carloni, P.FZJ* ; Rossetti, G.FZJ* ; Benvenuti, F. ; Bello, E. ; D’Incalci, M. ; Cappuzzello, E. ; Rosato, A. ; Del Sal, G. (Corresponding author)
A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action
Nature Communications 8, 15772 - (2017) [10.1038/ncomms15772]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Weichselbaum, E. ; Österbauer, M. ; Knyazev, D. G. ; Batishchev, O. V. ; Akimov, S. A. ; Hai Nguyen, T. ; Zhang, C. ; Knör, G. ; Agmon, N. ; Carloni, P.FZJ* ; Pohl, P. (Corresponding author)
Origin of proton affinity to membrane/water interfaces
Scientific reports 7(1), 4553 (2017) [10.1038/s41598-017-04675-9]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Minnerop, M.FZJ* ; Kurzwelly, D. (Corresponding author) ; Wagner, H. (Corresponding author) ; et al
Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia.
Brain 140(6), 1561 - 1578 (2017) [10.1093/brain/awx095]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Eckei, L. ; Krieg, S. ; Bütepage, M. ; Lehmann, A. ; Gross, A. ; Lippok, B. ; Grimm, A. R. ; Kümmerer, B. M. ; Rossetti, G.FZJ* ; Lüscher, B. (Corresponding author) ; Verheugd, P. (Corresponding author)
The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases
Scientific reports 7, 41746 - (2017) [10.1038/srep41746]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Villar-Piqué, A. ; Rossetti, G.FZJ* ; Ventura, S. ; Carloni, P.FZJ* ; Fernández, C. O. ; Outeiro, T. F. (Corresponding author)
Copper(II) and the pathological H50Q α-synuclein mutant: Environment meets genetics
Communicative & integrative biology 10(1), e1270484 - (2017) [10.1080/19420889.2016.1270484]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Hendriks, C. M. M. ; Hartkamp, J. ; Wiezorek, S. ; Steinkamp, A.-D. ; Rossetti, G.FZJ* ; Lüscher, B. ; Bolm, C. (Corresponding author)
Sulfoximines as ATR inhibitors: Analogs of VE-821
Bioorganic & medicinal chemistry letters 27(12), 2659 - 2662 (2017) [10.1016/j.bmcl.2017.04.026]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Casasnovas, R. ; Limongelli, V. ; Tiwary, P. ; Carloni, P. (Corresponding author)FZJ* ; Parrinello, M. (Corresponding author)
Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations
Journal of the American Chemical Society 139(13), 4780 - 4788 (2017) [10.1021/jacs.6b12950]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Sena, D. M. ; Cong, X. (Corresponding author) ; Giorgetti, A. ; Kless, A. ; Carloni, P. (Corresponding author)FZJ*
Structural heterogeneity of the $μ$-opioid receptor’s conformational ensemble in the apo state
Scientific reports 7, 45761 (2017) [10.1038/srep45761]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Nguyen, V. D. ; Nguyen, T. T. (Corresponding author) ; Carloni, P.FZJ*
DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions
Journal of biological physics 13(2), 185-195 (2017) [10.1007/s10867-017-9443-x]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Bochicchio, A.FZJ* ; Jordaan, S. ; Losasso, V. ; Chetty, S. ; Casasnovas Perera, R.FZJ* ; Ippoliti, E.FZJ* ; Barth, S. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation
Biomedicines 5(1), 9 (2017) [10.3390/biomedicines5010009]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Li, J.FZJ* ; Lyu, W.RWTH*FZJ* ; Rossetti, G.FZJ* ; Konijnenberg, A. ; Natalello, A. ; Ippoliti, E.FZJ* ; Orozco, M. ; Sobott, F. ; Grandori, R. ; Carloni, P. (Corresponding author)FZJ*
Proton Dynamics in Protein Mass Spectrometry
The journal of physical chemistry letters 8(6), 1105 - 1112 (2017) [10.1021/acs.jpclett.7b00127]2017 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Li, J.GRS Aachen* ; Vervoorts, J. ; Carloni, P.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Lüscher, B. (Corresponding author)
Structural prediction of the interaction of the tumor suppressor p27$^{KIP1}$ with cyclin A/CDK2 identifies a novel catalytically relevant determinant
BMC bioinformatics 18(1), 15 (2017) [10.1186/s12859-016-1411-0]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ponzoni, L. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ* ; Maggi, L. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Micheletti, C.
Unifying view of mechanical and functional hotspots across class A GPCRs
PLoS Computational Biology 13(2), e1005381 - (2017) [10.1371/journal.pcbi.1005381]2017 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Palermo, G. ; Favia, A. D. ; Convertino, M. ; De Vivo, M. (Corresponding author)FZJ*
The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition
ChemMedChem 11(12), 1252 - 1258 (2016) [10.1002/cmdc.201500507]2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Fahrenkamp, D. ; Li, J. ; Ernst, S. ; Schmitz-Van de Leur, H. ; Chatain, N. ; Küster, A. ; Koschmieder, S. ; Lüscher, B. ; Rossetti, G.FZJ* ; Müller-Newen, G. (Corresponding author)
Intramolecular hydrophobic interactions are critical mediators of STAT5 dimerization
Scientific reports 6, 35454 - (2016) [10.1038/srep35454]2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a book Dreyer, J.FZJ* ; Brancato, G. ; Ippoliti, E.FZJ* ; Genna, V. ; De Vivo, M.FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Rothlisberger, U.
Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics
2016Simulating Enzyme Reactivity / Tunon, Inaki (Editor) ; Cambridge : Royal Society of Chemistry, 2016, ; ISBN: ; doi:10.1039/9781782626831 Cambridge : Royal Society of Chemistry 294-339 (2016) [10.1039/9781782626831-00294]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Villar-Piqué, A. ; Lopes da Fonseca, T. ; Sant’Anna, R. ; Szegö, É. M. ; Fonseca-Ornelas, L. ; Pinho, R. ; Carija, A. ; Gerhardt, E. ; Masaracchia, C. ; Abad Gonzalez, E.GRS Aachen* ; Rossetti, G. ; Carloni, P.FZJ* ; Fernández, C. O. ; Foguel, D. ; Milosevic, I. ; Zweckstetter, M. ; Ventura, S. ; Outeiro, T. F. (Corresponding author)
Environmental and genetic factors support the dissociation between α-synuclein aggregation and toxicity
Proceedings of the National Academy of Sciences of the United States of America 113(42), E6506 - E6515 (2016) [10.1073/pnas.1606791113]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article La Sala, G. ; Riccardi, L. ; Gaspari, R. ; Cavalli, A. ; Hantschel, O. ; De Vivo, M. (Corresponding author)FZJ*
HRD Motif as the Central Hub of the Signaling Network for Activation Loop Autophosphorylation in Abl Kinase
Journal of chemical theory and computation 12(11), 5563 - 5574 (2016) [10.1021/acs.jctc.6b00600]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Genna, V. ; Vidossich, P. ; Ippoliti, E.FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Vivo, M. D. (Corresponding author)FZJ*
A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases
Journal of the American Chemical Society 138(44), 14592 - 14598 (2016) [10.1021/jacs.6b05475]2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G.FZJ* ; Musiani, F. ; Abad, E.FZJ* ; Dibenedetto, D.FZJ* ; Mouhib, H. ; Fernandez, C. O. ; Carloni, P. (Corresponding author)FZJ*
Conformational ensemble of human α-synuclein physiological form predicted by molecular simulations
Physical chemistry, chemical physics 18(8), 5702 - 5706 (2016) [10.1039/C5CP04549E]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kolář, M. H. (Corresponding author)FZJ* ; Hobza, P.
Computer Modeling of Halogen Bonds and Other σ-Hole Interactions
Chemical reviews 116(9), 5155 - 5187 (2016) [10.1021/acs.chemrev.5b00560]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article De Vivo, M. (Corresponding author)FZJ* ; Masetti, M. ; Bottegoni, G. ; Cavalli, A. (Corresponding author)
Role of Molecular Dynamics and Related Methods in Drug Discovery
Journal of medicinal chemistry 59(9), 4035 - 4061 (2016) [10.1021/acs.jmedchem.5b01684]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Genna, V. ; Gaspari, R. ; Dal Peraro, M. ; De Vivo, M. (Corresponding author)FZJ*
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η
Nucleic acids symposium series 44(6), 2827 - 2836 (2016) [10.1093/nar/gkw128]2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Pavlin, M. ; Rossetti, G. (Corresponding author)FZJ* ; De Vivo, M.FZJ* ; Carloni, P.FZJ*
Carnosine and Homocarnosine Degradation Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations
Biochemistry 55(19), 2772 - 2784 (2016) [10.1021/acs.biochem.5b01263]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Ghaemi, Z. ; Alberga, D. ; Carloni, P.FZJ* ; Laio, A. ; Lattanzi, G. (Corresponding author)
Permeability Coefficients of Lipophilic Compounds Estimated by Computer Simulations
Journal of chemical theory and computation 12(8), 4093 - 4099 (2016) [10.1021/acs.jctc.5b01126]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Cong, X.FZJ* ; Cremer, C. ; Nachreiner, T. ; Barth, S. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: Insights from enhanced sampling simulations
Protein science 25(8), 1451 - 1460 (2016) [10.1002/pro.2941]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Nguyen, T. T. ; Tran, D. P. ; Huy, P. D. Q. ; Hoang, Z. ; Carloni, P. (Corresponding author)FZJ* ; Van Pham, P. (Corresponding author) ; Nguyen, C. (Corresponding author) ; Li, M. S. (Corresponding author)
Ligand binding to anti-cancer target CD44 investigated by molecular simulations
Journal of molecular modeling 22(7), 165 (2016) [10.1007/s00894-016-3029-6]2016 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Park, K.-D. ; Muller, E. A. ; Kravtsov, V. ; Sass, P. M. ; Dreyer, J.FZJ* ; Atkin, J. M. ; Raschke, M. B. (Corresponding author)
Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics
Nano letters 16(1), 479 - 487 (2016) [10.1021/acs.nanolett.5b04135]2016 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Abad, E. ; Rossetti, G.FZJ*
Structural Predictions of Intrinsically Disordered Proteins with Computational Methods
2016NIC Symposium 2016
NIC Symposium 2016, JülichJülich, Germany, 11 Feb 2016 - 12 Feb 20162016-02-112016-02-12 Jülich : Forschungszentrum Jülich GmbH, Zentralbibliothek, NIC Series 48, 89-96 (2016)2016 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Li, J. ; Santambrogio, C. ; Brocca, S. ; Rossetti, G.FZJ* ; Carloni, P.FZJ* ; Grandori, R. (Corresponding author)
Conformational effects in protein electrospray-ionization mass spectrometry
Mass spectrometry reviews 35(1), 111 - 122 (2016) [10.1002/mas.21465]2016 BibTeX | EndNote: XML, Text | RIS

Contribution to a book Verma, R. S. (Editor) ; Bonavida, B. (Editor) ; Cremer, C.Extern* ; Hehmann-Titt, G. ; Schiffer, S. ; Melmer, G. ; Carloni, P.FZJ* ; Barth, S. (Corresponding author) ; Nachreiner, T.
Engineered Versions of Granzyme B and Angiogenin Overcome Intrinsic Resistance to Apoptosis Mediated by Human Cytolytic Fusion Proteins
2015Resistance to Immunotoxins in Cancer Therapy / Verma, Rama Shanker (Editor) ; Cham : Springer International Publishing, 2015, Chapter 8 ; ISSN: 2196-5501=2196-551X ; ISBN: 978-3-319-17274-3=978-3-319-17275-0 ; doi:10.1007/978-3-319-17275-0 Cham : Springer International Publishing, Resistance to Targeted Anti-Cancer Therapeutics 6, 185 - 219 (2015) [10.1007/978-3-319-17275-0_8]2015 BibTeX | EndNote: XML, Text | RIS

Journal Article Bolognesi, M. L. ; Bongarzone, S. ; Aulic, S. ; Ai Tran, H. N. ; Prati, F. ; Carloni, P.FZJ* ; Legname, G. (Corresponding author)
Rational approach to an antiprion compound with a multiple mechanism of action
Future medicinal chemistry 7(16), 2113 - 2120 (2015) [10.4155/fmc.15.79]2015 BibTeX | EndNote: XML, Text | RIS

Journal Article Cremer, C. ; Braun, H. ; Mladenov, R. ; Schenke, L. ; Cong, X. ; Jost, E. ; Brümmendorf, T. H. ; Fischer, R. ; Carloni, P.FZJ* ; Barth, S. ; Nachreiner, T. (Corresponding author)
Novel angiogenin mutants with increased cytotoxicity enhance the depletion of pro-inflammatory macrophages and leukemia cells ex vivo
Cancer immunology immunotherapy 64(12), 1575 - 1586 (2015) [10.1007/s00262-015-1763-8]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Palermo, G. ; Minniti, E. ; Greco, M. L. ; Riccardi, L. ; Simoni, E. ; Convertino, M. ; Marchetti, C. ; Rosini, M. ; Sissi, C. ; Minarini, A. ; De Vivo, M. (Corresponding author)FZJ*
An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512
Chemical communications 51(76), 14310 - 14313 (2015) [10.1039/C5CC05065K]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sedlak, R. ; Kolář, M. H.FZJ* ; Hobza, P. (Corresponding author)
Polar Flattening and the Strength of Halogen Bonding
Journal of chemical theory and computation 11(10), 4727 - 4732 (2015) [10.1021/acs.jctc.5b00687]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Giménez-Dejoz, J. ; Kolář, M. H.FZJ* ; Ruiz, F. X. ; Crespo, I. ; Cousido-Siah, A. ; Podjarny, A. ; Barski, O. A. ; Fanfrlík, J. ; Parés, X. ; Farrés, J. (Corresponding author) ; Porté, S. (Corresponding author)
Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase
PLoS one 10(7), e0134506 - (2015) [10.1371/journal.pone.0134506]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Fanfrlík, J. (Corresponding author) ; Ruiz, F. X. ; Kadlčíková, A. ; Řezáč, J. ; Cousido-Siah, A. ; Mitschler, A. ; Haldar, S. ; Lepšík, M. ; Kolář, M. H.FZJ* ; Majer, P. ; Podjarny, A. D. (Corresponding author) ; Hobza, P.
The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition
ACS chemical biology 10(7), 1637 - 1642 (2015) [10.1021/acschembio.5b00151]2015 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Kolář, M. H. ; Deepa, P. ; Ajani, H.FZJ* ; Pecina, A. ; Hobza, P. (Corresponding author)
Characteristics of a σ-Hole and the Nature of a Halogen Bond
2015Halogen Bonding II / Metrangolo, Pierangelo (Editor) Cham : Springer International Publishing, Topics in Current Chemistry 359, 1 - 25 (2015) [10.1007/128_2014_606]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Cong, X. ; Campomanes, P. ; Kless, A. ; Schapitz, I. ; Wagener, M. ; Koch, T. ; Carloni, P. (Corresponding author)FZJ*
Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor
PLoS one 10(8), e0135998 - (2015) [10.1371/journal.pone.0135998]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Calandrini, V. ; Rossetti, G. (Corresponding author)FZJ* ; Arnesano, F. ; Natile, G. ; Carloni, P.FZJ*
Computational metallomics of the anticancer drug cisplatin
Journal of inorganic biochemistry 153, 231 - 238 (2015) [10.1016/j.jinorgbio.2015.10.001]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Chatain, N. ; Perera, R. C. ; Rossetti, G.FZJ* ; Rossa, J. ; Carloni, P.FZJ* ; Schemionek, M. ; Haferlach, T. ; Brümmendorf, T. H. ; Schnittger, S. ; Koschmieder, S. (Corresponding author)
Rare FLT3 deletion mutants may provide additional treatment options to patients with AML: an approach to individualized medicine
Leukemia 29(12), 2434 - 2438 (2015) [10.1038/leu.2015.131]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Li, J. ; Flick, F. ; Verheugd, P. ; Carloni, P. ; Lüscher, B. ; Rossetti, G. (Corresponding author)FZJ*
Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2)
PLoS one 10(9), e0139095 - (2015) [10.1371/journal.pone.0139095]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G.FZJ* ; Dans, P. D. ; Gomez-Pinto, I. ; Ivani, I. ; Gonzalez, C. ; Orozco, M. (Corresponding author)
The structural impact of DNA mismatches
Nucleic acids symposium series 43(8), 4309 - 4321 (2015) [10.1093/nar/gkv254]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bochicchio, A. ; Rossetti, G. (Corresponding author)FZJ* ; Tabarrini, O. ; Krauβ, S. ; Carloni, P.FZJ*
Molecular View of Ligands Specificity for CAG Repeats in Anti-Huntington Therapy
Journal of chemical theory and computation 11(10), 4911 - 4922 (2015) [10.1021/acs.jctc.5b00208]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Finnerty, J. J. (Corresponding author)GRS Aachen* ; Peyser, A. (Corresponding author)FZJ* ; Carloni, P.FZJ*
Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation
PLoS one 10(10), e0138679 - (2015) [10.1371/journal.pone.0138679]2015 Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Cao, R.GRS Aachen* ; Rossetti, G. (Corresponding author)FZJ* ; Bauer, A.FZJ* ; Carloni, P.FZJ*
Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions
PLoS one 10(5), e0126833 (2015) [10.1371/journal.pone.0126833]2015 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Invited) Finnerty, J. (Corresponding author)GRS Aachen* ; Peyser, A.FZJ* ; Carloni, P.FZJ*
Statistical mechanical models for cation selectivity in biological channels
2015CECAM Workshop: Computational approaches to chemical senses, JülichJülich, Germany, 9 Sep 2015 - 11 Sep 20152015-09-092015-09-11 BibTeX | EndNote: XML, Text | RIS

Journal Article Sandal, M.GRS Aachen* ; Behrens, M. ; Brockhoff, A. ; Musiani, F. ; Giorgetti, A. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ* ; Meyerhof, W.
Evidence for a Transient Additional Ligand Binding Site in the TAS2R46 Bitter Taste Receptor
Journal of chemical theory and computation 11(9), 4439 - 4449 (2015) [10.1021/acs.jctc.5b00472]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Calligari, P. A. (Corresponding author) ; Calandrini, V.FZJ* ; Ollivier, J. ; Artero, J.-B. ; Härtlein, M. ; Johnson, M. (Corresponding author) ; Kneller, G. R. (Corresponding author)
Adaptation of Extremophilic Proteins with Temperature and Pressure: Evidence from Initiation Factor 6
The journal of physical chemistry <Washington, DC> / B 119(25), 7860 - 7873 (2015) [10.1021/acs.jpcb.5b02034]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Miotto, M. C. ; Valiente-Gabioud, A. A. ; Rossetti, G.FZJ* ; Zweckstetter, M. ; Carloni, P.FZJ* ; Selenko, P. ; Griesinger, C. ; Binolfi, A. (Corresponding author) ; Fernández, C. O. (Corresponding author)
Copper Binding to the N-Terminally Acetylated, Naturally Occurring Form of Alpha-Synuclein Induces Local Helical Folding
Journal of the American Chemical Society 137(20), 6444 - 6447 (2015) [10.1021/jacs.5b01911]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Arcella, A. ; Dreyer, J.FZJ* ; Ippoliti, E.FZJ* ; Ivani, I. ; Portella, G. ; Gabelica, V. ; Carloni, P.FZJ* ; Orozco, M. (Corresponding Author)
Structure and Dynamics of Oligonucleotides in the Gas Phase
Angewandte Chemie / International edition 54(2), 467–471 (2015) [10.1002/anie.201406910]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article D’Urzo, A. ; Konijnenberg, A. ; Rossetti, G.FZJ* ; Habchi, J. ; Li, J.FZJ* ; Carloni, P.FZJ* ; Sobott, F. ; Longhi, S. (Corresponding Author) ; Grandori, R. (Corresponding Author)
Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling
Journal of the American Society for Mass Spectrometry 26(3), 472 - 481 (2015) [10.1007/s13361-014-1048-z]2015 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G.FZJ* ; Dibenedetto, D.GRS* ; Calandrini, V.FZJ* ; Giorgetti, A. (Corresponding Author)GRS* ; Carloni, P.FZJ*
Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins
Archives of biochemistry and biophysics 582, 91–100 (2015) [10.1016/j.abb.2015.03.011]2015 Files BibTeX | EndNote: XML, Text | RIS

Conference Presentation (Other) Finnerty, J. J. (Corresponding author)GRS Aachen* ; Peyser, A.FZJ* ; Carloni, P.FZJ*
Ion Selectivity in Voltage-gated Biological Ion Channels
2014PAM SoftComp Topical Workshop: Proteins & Nanoparticles Membranes 2014, JülichJülich, Germany, 19 Oct 2014 - 22 Oct 20142014-10-192014-10-22 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Contribution to a conference proceedings Bochicchio, A. (Corresponding Author) ; Rossetti, G.FZJ* ; Musiani, F. ; Carloni, P.FZJ* ; Pantano, S. ; Krauss, S. ; Shah, N. J.FZJ*
Computer–aided design of ligands targeting RNA polyCAG expansion tracts in Huntington’s disease
2014International Prion Congress, Prion 2014, TriestTriest, Italy, 27 May 2014 - 30 May 20142014-05-272014-05-30 Austin, Tex. : Landes Bioscience 117 pp. (2014)2014 BibTeX | EndNote: XML, Text | RIS

Journal Article Calandrini, V.FZJ* ; Nguyen, T. H.GRS* ; Arnesano, F. ; Galliani, A. ; Ippoliti, E.FZJ* ; Carloni, P. (Corresponding Author)FZJ* ; Natile, G.
Structural Biology of Cisplatin Complexes with Cellular Targets: The Adduct with Human Copper Chaperone Atox1 in Aqueous Solution
Chemistry - a European journal 20(37), 11719 - 11725 (2014) [10.1002/chem.201402834]2014 BibTeX | EndNote: XML, Text | RIS

Journal Article Grison, A. ; Zucchelli, S. ; Urzì, A. ; Zamparo, I. ; Lazarevic, D. ; Pascarella, G. ; Roncaglia, P. ; Giorgetti, A.GRS* ; Garcia-Esparcia, P. ; Vlachouli, C. ; Simone, R. ; Persichetti, F. ; Forrest, A. R. ; Hayashizaki, Y. ; Carloni, P.FZJ* ; Ferrer, I. ; Lodovichi, C. ; Plessy, C. ; Carninci, P. (Corresponding Author) ; Gustincich, S. (Corresponding Author)
Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules
BMC genomics 15(1), 729 - (2014) [10.1186/1471-2164-15-729]2014 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kolář, M.GRS* ; Hostaš, J. ; Hobza, P. (Corresponding Author)
The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole
Physical chemistry, chemical physics 16(21), 9987 - (2014) [10.1039/c3cp55188a]2014 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Kolář, M. H. (Corresponding Author)GRS* ; Carloni, P.FZJ* ; Hobza, P.
Statistical analysis of σ-holes: a novel complementary view on halogen bonding
Physical chemistry, chemical physics 16(36), 19111 - (2014) [10.1039/C4CP02621G]2014 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Papamokos, G.GRS* ; Dreyer, J. (Corresponding Author)FZJ* ; Navarini, L. ; Carloni, P.FZJ*
Trapping acrylamide by a Michael addition: A computational study of the reaction between acrylamide and niacin
International journal of quantum chemistry 114(9), 553 - 559 (2014) [10.1002/qua.24610]2014 BibTeX | EndNote: XML, Text | RIS

Journal Article Calandrini, V.FZJ* ; Arnesano, F. ; Galliani, A. ; Nguyen, T. H.GRS* ; Ippoliti, E.FZJ* ; Carloni, P. (Corresponding Author)FZJ* ; Natile, G.
Platination of the copper transporter ATP7A involved in anticancer drug resistance
Dalton transactions 43(31), 12085 - (2014) [10.1039/C4DT01339E]2014 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Calandrini, V.FZJ* ; Dreyer, J.FZJ* ; Ippoliti, E. ; Carloni, P. (Corresponding Author)FZJ*
Hydration of chloride anions in the NanC Porin from Escherichia coli: A comparative study by QM/MM and MD simulations
The journal of chemical physics 141(22), 22D521 - (2014) [10.1063/1.4901111]2014 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Quy, V. (Corresponding Author) ; Carnevale, V. ; Manganaro, L. ; Lusic, M. ; Rossetti, G.FZJ* ; Leone, V. ; Fenollar-Ferrer, C. ; Raugei, S. ; Sal, G. ; Giacca, M. ; Carloni, P.FZJ*
HIV-1 Integrase Binding to its Cellular Partners: A Perspective from Computational Biology
Current pharmaceutical design 20(21), 3412 - 3421 (2014) [10.2174/13816128113199990631]2014 BibTeX | EndNote: XML, Text | RIS

Contribution to a book Musiani, F. ; Rossetti, G.FZJ* ; Giorgetti, A. (Corresponding Author) ; Carloni, P.FZJ*
Chemosensorial G-proteins-Coupled Receptors: A Perspective from Computational Methods
2014Protein Conformational Dynamics Cham : Springer International Publishing, Advances in Experimental Medicine and Biology 805, 441 - 457 (2014) [10.1007/978-3-319-02970-2_18]2014 BibTeX | EndNote: XML, Text | RIS

Journal Article Nguyen, T. H. ; Rossetti, G. (Corresponding Author)FZJ* ; Arnesano, F. ; Ippoliti, E.FZJ* ; Natile, G. ; Carloni, P.FZJ*
Molecular Recognition of Platinated DNA from Chromosomal HMGB1
Journal of chemical theory and computation 10(8), 3578 - 3584 (2014) [10.1021/ct500402e]2014 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Musiani, F. (Corresponding Author) ; Rossetti, G.FZJ* ; Capece, L. ; Gerger, T. M. ; Micheletti, C. ; Varani, G. ; Carloni, P.FZJ*
Molecular Dynamics Simulations Identify Time Scale of Conformational Changes Responsible for Conformational Selection in Molecular Recognition of HIV-1 Transactivation Responsive RNA
Journal of the American Chemical Society 136(44), 15631 - 15637 (2014) [10.1021/ja507812v]2014 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Stanyon, H. F. ; Cong, X.FZJ*GRS* ; Chen, Y. ; Shahidullah, N. ; Rossetti, G.FZJ* ; Dreyer, J.FZJ* ; Papamokos, G.GRS* ; Carloni, P.FZJ* ; Viles, J. H. (Corresponding Author)
Developing predictive rules for coordination geometry from visible circular dichroism of Copper(II) and Nickel(II) ions in histidine and amide main-chain complexes
The FEBS journal 281(17), 3945 - 3954 (2014) [10.1111/febs.12934]2014 Files BibTeX | EndNote: XML, Text | RIS

Contribution to a book Roberts, G. C. K. (Editor) ; Pietropaolo, A. (Corresponding Author) ; Carloni, P.FZJ*
Molecular Simulations of NGF Protein
2013Encyclopedia of Biophysics / Roberts, Gordon C. K. (Editor) Chapter 792 ; ISBN: 978-3-642-16711-9 ; doi:10.1007/978-3-642-16712-6 Berlin, Heidelberg : Springer Berlin Heidelberg 1590 - 1593 (2013) [10.1007/978-3-642-16712-6_792]2013 BibTeX | EndNote: XML, Text | RIS