• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5046680)   Today's Articles (1610)
For: Souza PCT, Alessandri R, Barnoud J, Thallmair S, Faustino I, Grünewald F, Patmanidis I, Abdizadeh H, Bruininks BMH, Wassenaar TA, Kroon PC, Melcr J, Nieto V, Corradi V, Khan HM, Domański J, Javanainen M, Martinez-Seara H, Reuter N, Best RB, Vattulainen I, Monticelli L, Periole X, Tieleman DP, de Vries AH, Marrink SJ. Martini 3: a general purpose force field for coarse-grained molecular dynamics. Nat Methods 2021;18:382-388. [PMID: 33782607 DOI: 10.1038/s41592-021-01098-3] [Citation(s) in RCA: 638] [Impact Index Per Article: 159.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 02/22/2021] [Indexed: 01/31/2023]
Number Cited by Other Article(s)
151
Srinivasan S, Álvarez D, John Peter AT, Vanni S. Unbiased MD simulations identify lipid binding sites in lipid transfer proteins. J Cell Biol 2024;223:e202312055. [PMID: 39105757 PMCID: PMC11303870 DOI: 10.1083/jcb.202312055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/29/2024] [Accepted: 07/16/2024] [Indexed: 08/07/2024]  Open
152
Li Y, Arghittu SM, Dietz MS, Hella GJ, Haße D, Ferraris DM, Freund P, Barth HD, Iamele L, de Jonge H, Niemann HH, Covino R, Heilemann M. Single-molecule imaging and molecular dynamics simulations reveal early activation of the MET receptor in cells. Nat Commun 2024;15:9486. [PMID: 39488533 PMCID: PMC11531568 DOI: 10.1038/s41467-024-53772-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 10/22/2024] [Indexed: 11/04/2024]  Open
153
Huang Z, Ni D, Chen Z, Zhu Y, Zhang W, Mu W. Application of molecular dynamics simulation in the field of food enzymes: improving the thermal-stability and catalytic ability. Crit Rev Food Sci Nutr 2024;64:11396-11408. [PMID: 37485919 DOI: 10.1080/10408398.2023.2238054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
154
Cao F, von Bülow S, Tesei G, Lindorff‐Larsen K. A coarse-grained model for disordered and multi-domain proteins. Protein Sci 2024;33:e5172. [PMID: 39412378 PMCID: PMC11481261 DOI: 10.1002/pro.5172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 07/12/2024] [Accepted: 08/23/2024] [Indexed: 10/20/2024]
155
Wang M, Guan Q, Wang C, Hu L, Hu X, Xu M, Cai Y, Zhang H, Cao Q, Sheng H, Wei X, Koehler JE, Dou H, Gu RX, Yuan C. Anchorage of bacterial effector at plasma membrane via selective phosphatidic acid binding to modulate host cell signaling. PLoS Pathog 2024;20:e1012694. [PMID: 39531410 PMCID: PMC11556746 DOI: 10.1371/journal.ppat.1012694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 10/24/2024] [Indexed: 11/16/2024]  Open
156
Chen X, Xu S, Chu B, Guo J, Zhang H, Sun S, Song L, Feng XQ. Applying Spatiotemporal Modeling of Cell Dynamics to Accelerate Drug Development. ACS NANO 2024;18:29311-29336. [PMID: 39420743 DOI: 10.1021/acsnano.4c12599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
157
Lou T, Zhuang X, Chang J, Gao Y, Bai X. Effect of Surface-Immobilized States of Antimicrobial Peptides on Their Ability to Disrupt Bacterial Cell Membrane Structure. J Funct Biomater 2024;15:315. [PMID: 39590519 PMCID: PMC11595214 DOI: 10.3390/jfb15110315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Revised: 10/21/2024] [Accepted: 10/23/2024] [Indexed: 11/28/2024]  Open
158
Li Y, Han R, Zhu B, Wang W, Song Z, Luo X. A Nonfouling Electrochemical Biosensor for Protein Analysis in Complex Body Fluids Based on Multifunctional Peptide Conjugated with PEGlyated Phospholipid. ACS Sens 2024;9:5596-5603. [PMID: 39415748 DOI: 10.1021/acssensors.4c02425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
159
Linhartova K, Falginella FL, Matl M, Sebesta M, Vácha R, Stefl R. Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7. Nat Commun 2024;15:9163. [PMID: 39448580 PMCID: PMC11502803 DOI: 10.1038/s41467-024-53305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 10/09/2024] [Indexed: 10/26/2024]  Open
160
Loose T, Sahrmann PG, Qu TS, Voth GA. Changing Your Martini Can Still Give You a Hangover. J Chem Theory Comput 2024;20:9190-9208. [PMID: 39361008 PMCID: PMC11500708 DOI: 10.1021/acs.jctc.4c00868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 09/25/2024] [Accepted: 09/27/2024] [Indexed: 10/23/2024]
161
Hornegger H, Anisimova AS, Muratovic A, Bourgeois B, Spinetti E, Niedermoser I, Covino R, Madl T, Karagöz GE. IGF2BP1 phosphorylation in the disordered linkers regulates ribonucleoprotein condensate formation and RNA metabolism. Nat Commun 2024;15:9054. [PMID: 39426983 PMCID: PMC11490574 DOI: 10.1038/s41467-024-53400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 10/11/2024] [Indexed: 10/21/2024]  Open
162
Bartocci A, Grazzi A, Awad N, Corringer PJ, Souza PCT, Cecchini M. A millisecond coarse-grained simulation approach to decipher allosteric cannabinoid binding at the glycine receptor α1. Nat Commun 2024;15:9040. [PMID: 39426952 PMCID: PMC11490541 DOI: 10.1038/s41467-024-53098-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/01/2024] [Indexed: 10/21/2024]  Open
163
Ivanova A, Atakpa-Adaji P, Rao S, Marti-Solano M, Taylor CW. Dual regulation of IP3 receptors by IP3 and PIP2 controls the transition from local to global Ca2+ signals. Mol Cell 2024;84:3997-4015.e7. [PMID: 39366376 DOI: 10.1016/j.molcel.2024.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 07/11/2024] [Accepted: 09/08/2024] [Indexed: 10/06/2024]
164
Noriega M, Corey RA, Haanappel E, Demange P, Czaplicki G, Atkinson RA, Chavent M. Coarse-Graining the Recognition of a Glycolipid by the C-Type Lectin Mincle Receptor. J Phys Chem B 2024;128:9935-9946. [PMID: 39368102 DOI: 10.1021/acs.jpcb.4c03242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
165
Pipatpadungsin N, Chao K, Rouse SL. Coarse-Grained Simulations of Adeno-Associated Virus and Its Receptor Reveal Influences on Membrane Lipid Organization and Curvature. J Phys Chem B 2024;128:10139-10153. [PMID: 39356546 PMCID: PMC11492248 DOI: 10.1021/acs.jpcb.4c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/21/2024] [Accepted: 09/17/2024] [Indexed: 10/03/2024]
166
Cofas-Vargas LF, Olivos-Ramirez GE, Chwastyk M, Moreira RA, Baker JL, Marrink SJ, Poma AB. Nanomechanical footprint of SARS-CoV-2 variants in complex with a potent nanobody by molecular simulations. NANOSCALE 2024;16:18824-18834. [PMID: 39351797 DOI: 10.1039/d4nr02074j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2024]
167
Qian R, Xue J, Xu Y, Huang J. Alchemical Transformations and Beyond: Recent Advances and Real-World Applications of Free Energy Calculations in Drug Discovery. J Chem Inf Model 2024;64:7214-7237. [PMID: 39360948 DOI: 10.1021/acs.jcim.4c01024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
168
Munafò I, Costa D, Milano G, Munaò G. Absorption of Polypropylene in Dipalmitoylphosphatidylcholine Membranes: The Role of Molecular Weight and Initial Configuration of Polymer Chains. J Phys Chem B 2024;128:9905-9916. [PMID: 39322978 DOI: 10.1021/acs.jpcb.4c05035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
169
Riedl S, Bilgen E, Agam G, Hirvonen V, Jussupow A, Tippl F, Riedl M, Maier A, Becker CFW, Kaila VRI, Lamb DC, Buchner J. Evolution of the conformational dynamics of the molecular chaperone Hsp90. Nat Commun 2024;15:8627. [PMID: 39366960 PMCID: PMC11452706 DOI: 10.1038/s41467-024-52995-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 09/25/2024] [Indexed: 10/06/2024]  Open
170
Introini B, Cui W, Chu X, Zhang Y, Alves AC, Eckhardt-Strelau L, Golusik S, Tol M, Vogel H, Yuan S, Kudryashev M. Structure of tetrameric forms of the serotonin-gated 5-HT3A receptor ion channel. EMBO J 2024;43:4451-4471. [PMID: 39232129 PMCID: PMC11480441 DOI: 10.1038/s44318-024-00191-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 09/06/2024]  Open
171
Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO J 2024;43:4668-4698. [PMID: 39232130 PMCID: PMC11480506 DOI: 10.1038/s44318-024-00207-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/02/2024] [Accepted: 07/23/2024] [Indexed: 09/06/2024]  Open
172
Baksi A, Zerze H, Agrawal A, Karim A, Zerze GH. The molecular picture of the local environment in a stable model coacervate. Commun Chem 2024;7:222. [PMID: 39349768 PMCID: PMC11442467 DOI: 10.1038/s42004-024-01304-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 09/11/2024] [Indexed: 10/04/2024]  Open
173
Richardson JD, Van Lehn RC. Free Energy Analysis of Peptide-Induced Pore Formation in Lipid Membranes by Bridging Atomistic and Coarse-Grained Simulations. J Phys Chem B 2024;128:8737-8752. [PMID: 39207202 DOI: 10.1021/acs.jpcb.4c03276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
174
Varma SG, Mitra A, Sarkar S. Self-diffusion is temperature independent on active membranes. Phys Chem Chem Phys 2024;26:23348-23362. [PMID: 39211961 DOI: 10.1039/d4cp02470b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
175
Neubergerová M, Pleskot R. Plant protein-lipid interfaces studied by molecular dynamics simulations. JOURNAL OF EXPERIMENTAL BOTANY 2024;75:5237-5250. [PMID: 38761107 DOI: 10.1093/jxb/erae228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/16/2024] [Indexed: 05/20/2024]
176
Prabhu J, Frigerio M, Petretto E, Campomanes P, Salentinig S, Vanni S. A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions. J Chem Theory Comput 2024;20:7624-7634. [PMID: 39160094 PMCID: PMC11391577 DOI: 10.1021/acs.jctc.4c00529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
177
Korshunova K, Kiuru J, Liekkinen J, Enkavi G, Vattulainen I, Bruininks BMH. Martini 3 OliGo̅mers: A Scalable Approach for Multimers and Fibrils in GROMACS. J Chem Theory Comput 2024;20:7635-7645. [PMID: 39189419 PMCID: PMC11391574 DOI: 10.1021/acs.jctc.4c00677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
178
Coker JF, Moro S, Gertsen AS, Shi X, Pearce D, van der Schelling MP, Xu Y, Zhang W, Andreasen JW, Snyder CR, Richter LJ, Bird MJ, McCulloch I, Costantini G, Frost JM, Nelson J. Perpendicular crossing chains enable high mobility in a noncrystalline conjugated polymer. Proc Natl Acad Sci U S A 2024;121:e2403879121. [PMID: 39226361 PMCID: PMC11406284 DOI: 10.1073/pnas.2403879121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 07/22/2024] [Indexed: 09/05/2024]  Open
179
Kim S. All-Atom Membrane Builder via Multiscale Simulation. J Chem Inf Model 2024. [PMID: 39250520 DOI: 10.1021/acs.jcim.4c01059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
180
Zhang G, Chu X. Balancing thermodynamic stability, dynamics, and kinetics in phase separation of intrinsically disordered proteins. J Chem Phys 2024;161:095102. [PMID: 39225535 DOI: 10.1063/5.0220861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024]  Open
181
Ishizuka R. Martini 3D-OZ: A Theoretical Investigation of Solvation Shell Structures and Solvation Free Energies of Martini Coarse-Grained Proteins. J Phys Chem B 2024;128:8522-8529. [PMID: 39180742 DOI: 10.1021/acs.jpcb.4c03897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
182
Pedersen KB, Borges-Araújo L, Stange AD, Souza PCT, Marrink SJ, Schiøtt B. OLIVES: A Go̅-like Model for Stabilizing Protein Structure via Hydrogen Bonding Native Contacts in the Martini 3 Coarse-Grained Force Field. J Chem Theory Comput 2024. [PMID: 39235392 DOI: 10.1021/acs.jctc.4c00553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2024]
183
Khodam Hazrati M, Vácha R. Membrane Adsorption Enhances Translocation of Antimicrobial Peptide Buforin 2. J Phys Chem B 2024;128:8469-8476. [PMID: 39194157 PMCID: PMC11382259 DOI: 10.1021/acs.jpcb.4c04338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 07/31/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
184
Pabois O, Dong Y, Kampf N, Lorenz CD, Doutch J, Avila-Sierra A, Ramaioli M, Mu M, Message Y, Liamas E, Tyler AII, Klein J, Sarkar A. Self-assembly of sustainable plant protein protofilaments into a hydrogel for ultra-low friction across length scales. COMMUNICATIONS MATERIALS 2024;5:158. [PMID: 39238825 PMCID: PMC11371639 DOI: 10.1038/s43246-024-00590-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/25/2024] [Indexed: 09/07/2024]
185
Beigl TB, Paul A, Fellmeth TP, Nguyen D, Barber L, Weller S, Schäfer B, Gillissen BF, Aulitzky WE, Kopp HG, Rehm M, Andrews DW, Pluhackova K, Essmann F. BCL-2 and BOK regulate apoptosis by interaction of their C-terminal transmembrane domains. EMBO Rep 2024;25:3896-3924. [PMID: 39048751 PMCID: PMC11387410 DOI: 10.1038/s44319-024-00206-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/27/2024]  Open
186
Yang R, Bernardino K, Xiao X, Gomes WR, Mattoso DA, Kotov NA, Bogdan P, de Moura AF. Graph Theoretical Description of Phase Transitions in Complex Multiscale Phases with Supramolecular Assemblies. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2402464. [PMID: 38952077 PMCID: PMC11967988 DOI: 10.1002/advs.202402464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/15/2024] [Indexed: 07/03/2024]
187
Eubanks E, VanderSleen K, Mody J, Patel N, Sacks B, Farahani MD, Wang J, Elliott J, Jaber N, Akçimen F, Bandres-Ciga S, Helweh F, Liu J, Archakam S, Kimelman R, Sharma B, Socha P, Guntur A, Bartels T, Dettmer U, Mouradian MM, Bahrami AH, Dai W, Baum J, Shi Z, Hardy J, Kara E. Increased burden of rare risk variants across gene expression networks predisposes to sporadic Parkinson's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610195. [PMID: 39257816 PMCID: PMC11384021 DOI: 10.1101/2024.08.30.610195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
188
Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse, shedding light on the dark matter of molecular dynamics simulations. eLife 2024;12:RP90061. [PMID: 39212001 PMCID: PMC11364437 DOI: 10.7554/elife.90061] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]  Open
189
Petruk G, Petrlova J, Samsudin F, Bond PJ, Schmidtchen A. Thrombin-derived C-terminal peptides bind and form aggregates with sulfated glycosaminoglycans. Heliyon 2024;10:e35703. [PMID: 39229523 PMCID: PMC11369470 DOI: 10.1016/j.heliyon.2024.e35703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/05/2024]  Open
190
Kolmangadi MA, Wani YM, Schönhals A, Nikoubashman A. Coarse-Grained Simulations of Columnar Ionic Liquid Crystals: Comparison with Experiments. J Phys Chem B 2024;128:8215-8222. [PMID: 39163525 DOI: 10.1021/acs.jpcb.4c03041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
191
Iannetti L, Cambiaso S, Rasera F, Giacomello A, Rossi G, Bochicchio D, Tinti A. The surface tension of Martini 3 water mixtures. J Chem Phys 2024;161:084707. [PMID: 39189655 DOI: 10.1063/5.0221199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Accepted: 07/17/2024] [Indexed: 08/28/2024]  Open
192
Mayar S, Borbuliak M, Zoumpoulakis A, Bouceba T, Labonté MM, Ahrari A, Sinniah N, Memarpoor-Yazdi M, Vénien-Bryan C, Tieleman DP, D'Avanzo N. Endocannabinoid regulation of inward rectifier potassium (Kir) channels. Front Pharmacol 2024;15:1439767. [PMID: 39253376 PMCID: PMC11381239 DOI: 10.3389/fphar.2024.1439767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 08/12/2024] [Indexed: 09/11/2024]  Open
193
van Gunsteren WF, Oostenbrink C. Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J Chem Inf Model 2024;64:6281-6304. [PMID: 39136351 DOI: 10.1021/acs.jcim.4c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
194
Wang Y, Zou R, Zhou Y, Zheng Y, Peng C, Liu Y, Tan H, Fu Q, Ding M. Unraveling mechanisms of protein encapsulation and release in coacervates via molecular dynamics and machine learning. Chem Sci 2024;15:13442-13451. [PMID: 39183928 PMCID: PMC11339950 DOI: 10.1039/d4sc03061c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/22/2024] [Indexed: 08/27/2024]  Open
195
Nemchinova M, Schuurman-Wolters GK, Whittaker JJ, Arkhipova V, Marrink SJ, Poolman B, Guskov A. Exploring the Ligand Binding and Conformational Dynamics of the Substrate-Binding Domain 1 of the ABC Transporter GlnPQ. J Phys Chem B 2024;128:7822-7832. [PMID: 39090964 PMCID: PMC11331510 DOI: 10.1021/acs.jpcb.4c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/21/2024] [Accepted: 07/25/2024] [Indexed: 08/04/2024]
196
Yu Y, Liu Q, Zeng J, Tan Y, Tang Y, Wei G. Multiscale simulations reveal the driving forces of p53C phase separation accelerated by oncogenic mutations. Chem Sci 2024;15:12806-12818. [PMID: 39148776 PMCID: PMC11323318 DOI: 10.1039/d4sc03645j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/07/2024] [Indexed: 08/17/2024]  Open
197
Ye BB, Chen S, Wang ZG. GCMe: Efficient Implementation of the Gaussian Core Model with Smeared Electrostatic Interactions for Molecular Dynamics Simulations of Soft Matter Systems. J Chem Theory Comput 2024;20:6870-6880. [PMID: 39013595 PMCID: PMC11325544 DOI: 10.1021/acs.jctc.4c00603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
198
Brandner AF, Prakaash D, Blanco González A, Waterhouse F, Khalid S. Faster but Not Sweeter: A Model of Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 Version with Accelerated Kinetics. J Chem Theory Comput 2024;20:6890-6903. [PMID: 39008538 PMCID: PMC11325540 DOI: 10.1021/acs.jctc.4c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
199
Martins G, Galamba N. Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study. J Chem Inf Model 2024;64:6115-6131. [PMID: 39046235 PMCID: PMC11323248 DOI: 10.1021/acs.jcim.4c00965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/25/2024]
200
Thomasen FE, Skaalum T, Kumar A, Srinivasan S, Vanni S, Lindorff-Larsen K. Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution. Nat Commun 2024;15:6645. [PMID: 39103332 DOI: 10.1038/s41467-024-50647-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/15/2024] [Indexed: 08/07/2024]  Open
PrevPage 4 of 13 123451213Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA