Institute of Neurosciences and Medicine (INM)

Computational Biomedicine (INM-9)

Publications of IAS-5/INM-9 in 2024

Journal Article Carloni, P. (Corresponding author)FZJ* ; Sanbonmatsu, K. (Corresponding author)Extern*
Exascale simulations and beyond
Current opinion in structural biology 89, 102939 - (2024) [10.1016/j.sbi.2024.102939]2024 BibTeX | EndNote: XML, Text | RIS

Journal Article Schimunek, J. ; Seidl, P. ; Elez, K. ; et al
A community effort to discover small molecule SARS-CoV-2 inhibitors
Molecular informatics 43(1), e202300262 (2024) [10.1002/minf.202300262]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Ortega-Ramírez, A. M. ; Albani, S.FZJ* ; Bachmann, M. ; Schmidt, A. ; Pinoé-Schmidt, M. ; Assmann, M. ; Augustinowski, K. ; Rossetti, G.FZJ* ; Gründer, S. (Corresponding author)
A conserved peptide-binding pocket in HyNaC/ASIC ion channels
Proceedings of the National Academy of Sciences of the United States of America 121(41), e2409097121 (2024) [10.1073/pnas.2409097121]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Xie, S.FZJ* ; Zuo, K. (Corresponding author)FZJ* ; De Rubeis, S. ; Ruggerone, P. (Corresponding author) ; Carloni, P. (Corresponding author)FZJ*
Molecular basis of the CYFIP2 and NCKAP1 autism-linked variants in the WAVE regulatory complex
[10.26434/chemrxiv-2024-x3sn8] OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Talk (non-conference) (Invited) Bergeest, C. (Corresponding author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Rizzi, A.FZJ* ; Mandelli, D.FZJ* ; Assent, I.FZJ* ; Berlage, T. ; Rossetti, G.FZJ*
Data-Driven Approaches to Rational Design of Covalent Drugs
2024Annual HDS-LEE Retreat, RWTH AachenJülich, RWTH Aachen, Germany, 9 Sep 2024 - 10 Sep 20242024-09-092024-09-10 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Bergeest, C. (First author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Rizzi, A.FZJ* ; Mandelli, D.FZJ* ; Assent, I.FZJ* ; Berlage, T. ; Rossetti, G. (Corresponding author)FZJ*
From Covalent Docking to QM/MM Simulations: A continuous Pipeline using Snakemake
2024INM Retreat 2024, RWTH AachenJülich, RWTH Aachen, Germany, 19 Nov 2024 - 20 Nov 20242024-11-192024-11-20 BibTeX | EndNote: XML, Text | RIS

Poster (Invited) Bergeest, C. (First author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Rizzi, A.FZJ* ; Mandelli, D.FZJ* ; Assent, I.FZJ* ; Berlage, T. ; Rossetti, G. (Corresponding author)FZJ*
From Covalent Docking to QM/MM Simulations: A continuous Pipeline using Snakemake
2024INM-9 Internal Workshop 2024, RWTH AachenLandgraaf, RWTH Aachen, Netherlands, 28 Oct 2024 - 29 Oct 20242024-10-282024-10-29 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Bergeest, C. (First author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Rizzi, A.FZJ* ; Mandelli, D.FZJ* ; Assent, I.FZJ* ; Berlage, T. ; Rossetti, G. (Corresponding author)FZJ*
From Covalent Docking to QM/MM Simulations: A continuous Pipeline using Snakemake
202424th European Symposium on Quantitative Structure-Activity Relationship - Synergizing AI and Multiscale Modeling for Drug Discovery, EuroQSAR 2024, RWTH AachenBarcelona, RWTH Aachen, Spain, 22 Sep 2024 - 26 Sep 20242024-09-222024-09-26 BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Bergeest, C. (First author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Rizzi, A.FZJ* ; Mandelli, D.FZJ* ; Assent, I.FZJ* ; Berlage, T. ; Rossetti, G. (Corresponding author)FZJ*
Unveiling the Challenges of Covalent Docking: A Computational Analysis on SARS-CoV 2 MPro Inhibitors
2024The 4th Molecules Medicinal Chemistry Symposium - Harnessing the Power of New Drug Modalities, MMCS, RWTH AachenBarcelona, RWTH Aachen, Spain, 24 Apr 2024 - 26 Apr 20242024-04-242024-04-26 BibTeX | EndNote: XML, Text | RIS

Dataset de Bruyn, E. (First author)FZJ*RWTH* ; Dorn, A. (First author)FZJ* ; Rossetti, G. (Corresponding author)FZJ*RWTH* ; Fernandez, C. O. ; Outeiro, T. F. ; Schulz, J. B.FZJ*RWTH* ; Carloni, P. (Last author)FZJ*RWTH*
Molecular Dynamics Trajectories Exploring the Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution
Jülich : Forschungszentrum Jülich (2024) [10.5281/zenodo.12605635]2024 Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Nägele, G.FZJ*
Quasi-two-dimensional dispersions of Brownian particles with competitive interactions: phase behavior and structural properties
Soft matter 20(48), 9528-9546 (2024) [10.1039/D4SM00736K]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Patent Carloni, P.FZJ* ; Rossetti, G.FZJ* ; Barth, S. ; Akinrinmade, O. A. ; Daramola, A. K. ; Chetty, S. ; Goßen, J. ; Naran, K.
DEIMMUNIZED PSEUDOMONAS EXOTOXIN A
Fulltext BibTeX | EndNote: XML, Text | RIS

Journal Article de Bruyn, E. (First author)FZJ*RWTH* ; Dorn, A. E. (First author)FZJ* ; Rossetti, G. (Corresponding author)FZJ*RWTH* ; Fernandez, C.Extern* ; Outeiro, T. F.Extern* ; Schulz, J. B.FZJ* ; Carloni, P. (Last author)FZJ*RWTH*
Impact of Phosphorylation on the Physiological Form of Human alpha-Synuclein in Aqueous Solution
Journal of chemical information and modeling 64(21), 8215–8226 (2024) [10.1021/acs.jcim.4c01172]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Preprint Dmitrieva, N.FZJ* ; Gholami, S.FZJ* ; Alleva, C. ; Carloni, P.FZJ* ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; Fahlke, C. (Corresponding author)FZJ*
Transport mechanism of DgoT, a bacterial homolog of SLC17 organic anion transporters
Hoboken, NJ [u.a.] : Wiley (2024)2024 DBCoverage BibTeX | EndNote: XML, Text | RIS

Journal Article Maleeva, G. ; Nin-Hill, A. ; Wirth, U. ; Rustler, K. ; Ranucci, M. ; Opar, E. ; Rovira, C. ; Bregestovski, P. ; Zeilhofer, H. U. ; König, B. ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; Gorostiza, P. (Corresponding author)
Light-Activated Agonist-Potentiator of GABA A Receptors for Reversible Neuroinhibition in Wildtype Mice
Journal of the American Chemical Society 146(42), 28822-28831 (2024) [10.1021/jacs.4c08446]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Salvadori, G. (Corresponding author)FZJ* ; Mennucci, B. (Corresponding author)
Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling
The journal of physical chemistry letters 15(31), 8078 - 8084 (2024) [10.1021/acs.jpclett.4c01823]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Albani, S.FZJ* ; Eswaran, V. S. B. ; Piergentili, A.FZJ* ; de Souza, P. C. T. ; Lampert, A. (Corresponding author) ; Rossetti, G. (Corresponding author)FZJ*
Depletion of membrane cholesterol modifies structure, dynamic and activation of Nav1.7
International journal of biological macromolecules 278, 134219 - (2024) [10.1016/j.ijbiomac.2024.134219]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Diaz-Pier, S. (Corresponding author)FZJ* ; Carloni, P.FZJ*
Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives
Current opinion in structural biology 87, 102817 (2024) [10.1016/j.sbi.2024.102817]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G.FZJ* ; Mandelli, D. (Corresponding author)FZJ*
How exascale computing can shape drug design: A perspective from multiscale QM/MM molecular dynamics simulations and machine learning-aided enhanced sampling algorithms
Current opinion in structural biology 86, 102814 - (2024) [10.1016/j.sbi.2024.102814]2024 OpenAccess Files BibTeX | EndNote: XML, Text | RIS

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 Mandelli, D. (Corresponding author)FZJ*
Effective Data-Driven Collective Variables for Free Energy Calculations from Metadynamics of Paths
PNAS nexus 3(4), 159 (2024) [10.1093/pnasnexus/pgae159]2024 OpenAccess Files 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

Last Modified: 21.01.2025