Publications of IAS-5/INM-9 in 2023

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

Last Modified: 21.01.2025