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For: Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE. Biomolecular simulation: a computational microscope for molecular biology. Annu Rev Biophys 2013;41:429-52. [PMID: 22577825 DOI: 10.1146/annurev-biophys-042910-155245] [Citation(s) in RCA: 769] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Number Cited by Other Article(s)
151
Neel BL, Nisler CR, Walujkar S, Araya-Secchi R, Sotomayor M. Elastic versus brittle mechanical responses predicted for dimeric cadherin complexes. Biophys J 2022;121:1013-1028. [PMID: 35151631 PMCID: PMC8943749 DOI: 10.1016/j.bpj.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022]  Open
152
Neel BL, Nisler CR, Walujkar S, Araya-Secchi R, Sotomayor M. Collective mechanical responses of cadherin-based adhesive junctions as predicted by simulations. Biophys J 2022;121:991-1012. [PMID: 35150618 PMCID: PMC8943820 DOI: 10.1016/j.bpj.2022.02.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 12/13/2022]  Open
153
Yu CH, Chen W, Chiang YH, Guo K, Martin Moldes Z, Kaplan DL, Buehler MJ. End-to-End Deep Learning Model to Predict and Design Secondary Structure Content of Structural Proteins. ACS Biomater Sci Eng 2022;8:1156-1165. [PMID: 35129957 PMCID: PMC9347213 DOI: 10.1021/acsbiomaterials.1c01343] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
154
Das J, Mahammad FS, Krishnamurthy RG. An integrated chemo-informatics and in vitro experimental approach repurposes acarbose as a post-ischemic neuro-protectant. 3 Biotech 2022;12:71. [PMID: 35223357 PMCID: PMC8847516 DOI: 10.1007/s13205-022-03130-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/23/2022] [Indexed: 11/26/2022]  Open
155
Patel D, Haag SL, Patel JS, Ytreberg FM, Bernards MT. Paired Simulations and Experimental Investigations into the Calcium-Dependent Conformation of Albumin. J Chem Inf Model 2022;62:1282-1293. [PMID: 35194993 DOI: 10.1021/acs.jcim.1c01104] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
156
Molecular Dynamics Simulations of Protein Aggregation: Protocols for Simulation Setup and Analysis with Markov State Models and Transition Networks. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022;2340:235-279. [PMID: 35167078 DOI: 10.1007/978-1-0716-1546-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
157
Song W, Corey RA, Ansell TB, Cassidy CK, Horrell MR, Duncan AL, Stansfeld PJ, Sansom MSP. PyLipID: A Python Package for Analysis of Protein-Lipid Interactions from Molecular Dynamics Simulations. J Chem Theory Comput 2022;18:1188-1201. [PMID: 35020380 PMCID: PMC8830038 DOI: 10.1021/acs.jctc.1c00708] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 12/11/2022]
158
Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM. Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022;70:934-943. [PMID: 34990125 DOI: 10.1021/acs.jafc.1c06110] [Citation(s) in RCA: 176] [Impact Index Per Article: 58.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
159
Sengul MY, MacKerell AD. Accurate Modeling of RNA Hairpins Through the Explicit Treatment of Electronic Polarizability with the Classical Drude Oscillator Force Field. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2022;21:461-471. [DOI: 10.1142/s2737416521420060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
160
Wang J, Yu Y, Leng T, Li Y, Lee ST. The Inhibition of SARS-CoV-2 3CL Mpro by Graphene and Its Derivatives from Molecular Dynamics Simulations. ACS APPLIED MATERIALS & INTERFACES 2022;14:191-200. [PMID: 34933561 PMCID: PMC8713398 DOI: 10.1021/acsami.1c18104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
161
Chen J, Liu H, Cui X, Li Z, Chen HF. RNA-Specific Force Field Optimization with CMAP and Reweighting. J Chem Inf Model 2022;62:372-385. [PMID: 35021622 DOI: 10.1021/acs.jcim.1c01148] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
162
Tolmachev D, Lukasheva N, Ramazanov R, Nazarychev V, Borzdun N, Volgin I, Andreeva M, Glova A, Melnikova S, Dobrovskiy A, Silber SA, Larin S, de Souza RM, Ribeiro MCC, Lyulin S, Karttunen M. Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives. Int J Mol Sci 2022;23:645. [PMID: 35054840 PMCID: PMC8775846 DOI: 10.3390/ijms23020645] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022]  Open
163
Chen CH, Pepper K, Ulmschneider JP, Ulmschneider MB, Lu TK. Predicting Membrane-Active Peptide Dynamics in Fluidic Lipid Membranes. Methods Mol Biol 2022;2405:115-136. [PMID: 35298811 DOI: 10.1007/978-1-0716-1855-4_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] [Indexed: 06/14/2023]
164
Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022;7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023]  Open
165
Moreira RA, Baker JL, Guzman HV, Poma AB. Assessing the Stability of Biological Fibrils by Molecular-Scale Simulations. Methods Mol Biol 2022;2340:357-378. [PMID: 35167082 DOI: 10.1007/978-1-0716-1546-1_16] [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: 06/14/2023]
166
González-Fernández C, Bringas E, Oostenbrink C, Ortiz I. In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come? Comput Struct Biotechnol J 2022;20:5886-5901. [PMID: 36382192 PMCID: PMC9636410 DOI: 10.1016/j.csbj.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022]  Open
167
Banerjee A, Lu CY, Dutt M. A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides. Phys Chem Chem Phys 2021;24:1553-1568. [PMID: 34940778 DOI: 10.1039/d1cp04205j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
168
Chang L, Perez A, Miranda-Quintana RA. Improving the analysis of biological ensembles through extended similarity measures. Phys Chem Chem Phys 2021;24:444-451. [PMID: 34897334 DOI: 10.1039/d1cp04019g] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
169
Abrol R, Serrano E, Santiago LJ. Development of enhanced conformational sampling methods to probe the activation landscape of GPCRs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021;128:325-359. [PMID: 35034722 PMCID: PMC11476118 DOI: 10.1016/bs.apcsb.2021.11.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
170
Ahn SH, Ojha AA, Amaro RE, McCammon JA. Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling. J Chem Theory Comput 2021;17:7938-7951. [PMID: 34844409 DOI: 10.1021/acs.jctc.1c00770] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
171
Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021;84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
172
Kapakayala AB, Nair NN. Boosting the conformational sampling by combining replica exchange with solute tempering and well-sliced metadynamics. J Comput Chem 2021;42:2233-2240. [PMID: 34585768 DOI: 10.1002/jcc.26752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/30/2021] [Accepted: 09/12/2021] [Indexed: 01/22/2023]
173
Kekez M, Zanki V, Antičević I, Rokov-Plavec J, Maršavelski A. Importance of protein intrinsic conformational dynamics and transient nature of non-covalent interactions in ligand binding affinity. Int J Biol Macromol 2021;192:692-700. [PMID: 34655583 DOI: 10.1016/j.ijbiomac.2021.10.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022]
174
Foloppe N, Chen IJ. The reorganization energy of compounds upon binding to proteins, from dynamic and solvated bound and unbound states. Bioorg Med Chem 2021;51:116464. [PMID: 34798378 DOI: 10.1016/j.bmc.2021.116464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022]
175
Li M, Wen J, Huang X, Nie Q, Wu X, Ma W, Nie S, Xie M. Interaction between polysaccharides and toll-like receptor 4: Primary structural role, immune balance perspective, and 3D interaction model hypothesis. Food Chem 2021;374:131586. [PMID: 34839969 DOI: 10.1016/j.foodchem.2021.131586] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022]
176
Lee BH, Park SW, Jo S, Kim MK. Protein conformational transitions explored by a morphing approach based on normal mode analysis in internal coordinates. PLoS One 2021;16:e0258818. [PMID: 34735476 PMCID: PMC8568156 DOI: 10.1371/journal.pone.0258818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022]  Open
177
Edwards T, Foloppe N, Harris SA, Wells G. The future of biomolecular simulation in the pharmaceutical industry: what we can learn from aerodynamics modelling and weather prediction. Part 1. understanding the physical and computational complexity of in silico drug design. Acta Crystallogr D Struct Biol 2021;77:1348-1356. [PMID: 34726163 PMCID: PMC8561735 DOI: 10.1107/s2059798321009712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 09/17/2021] [Indexed: 02/04/2023]  Open
178
González-Fernández C, Basauri A, Fallanza M, Bringas E, Oostenbrink C, Ortiz I. Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J Chem Inf Model 2021;61:4839-4851. [PMID: 34559524 PMCID: PMC8549069 DOI: 10.1021/acs.jcim.1c00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
179
Yu Y, Klauda JB. Symmetric and Asymmetric Models for the Arabidopsis thaliana Plasma Membrane: A Simulation Study. J Phys Chem B 2021;125:11418-11431. [PMID: 34617773 DOI: 10.1021/acs.jpcb.1c04704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
180
Lin Y, Buyan A, Corry B. Computational studies of Piezo1 yield insights into key lipid–protein interactions, channel activation, and agonist binding. Biophys Rev 2021;14:209-219. [DOI: 10.1007/s12551-021-00847-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/20/2021] [Indexed: 12/21/2022]  Open
181
Choi B, Kim NH, Jin GY, Kim YS, Kim YH, Eom K. Sequence-dependent aggregation-prone conformations of islet amyloid polypeptide. Phys Chem Chem Phys 2021;23:22532-22542. [PMID: 34590645 DOI: 10.1039/d1cp01061a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
182
Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. J Chem Theory Comput 2021;17:6491-6508. [PMID: 34506133 DOI: 10.1021/acs.jctc.1c00414] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
183
On the human taste perception: Molecular-level understanding empowered by computational methods. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
184
Şterbuleac D. Molecular dynamics: a powerful tool for studying the medicinal chemistry of ion channel modulators. RSC Med Chem 2021;12:1503-1518. [PMID: 34671734 PMCID: PMC8459385 DOI: 10.1039/d1md00140j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/21/2021] [Indexed: 01/10/2023]  Open
185
Andújar SA, Gutiérrez LJ, Enriz RD, Baldoni HA. Structure, interface stability and hot-spots identification for RBD(SARS-CoV-2):hACE2 complex formation. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.1979229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
186
Jas GS, Childs EW, Middaugh CR, Kuczera K. Dissecting Multiple Pathways in the Relaxation Dynamics of Helix <==> Coil Transitions with Optimum Dimensionality Reduction. Biomolecules 2021;11:1351. [PMID: 34572564 PMCID: PMC8471320 DOI: 10.3390/biom11091351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/07/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]  Open
187
Kamenik AS, Singh I, Lak P, Balius TE, Liedl KR, Shoichet BK. Energy penalties enhance flexible receptor docking in a model cavity. Proc Natl Acad Sci U S A 2021;118:e2106195118. [PMID: 34475217 PMCID: PMC8433570 DOI: 10.1073/pnas.2106195118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022]  Open
188
Mitxelena I, López X, de Sancho D. Markov state models from hierarchical density-based assignment. J Chem Phys 2021;155:054102. [PMID: 34364321 DOI: 10.1063/5.0056748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
189
Chen Y, Krämer A, Charron NE, Husic BE, Clementi C, Noé F. Machine learning implicit solvation for molecular dynamics. J Chem Phys 2021;155:084101. [PMID: 34470360 DOI: 10.1063/5.0059915] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
190
Dong T, Gong T, Li W. Accurate Estimation of Solvent Accessible Surface Area for Coarse-Grained Biomolecular Structures with Deep Learning. J Phys Chem B 2021;125:9490-9498. [PMID: 34383495 DOI: 10.1021/acs.jpcb.1c05203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
191
Kuroda D, Tsumoto K. Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease. Biophys Physicobiol 2021;18:215-222. [PMID: 34631338 PMCID: PMC8470906 DOI: 10.2142/biophysico.bppb-v18.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022]  Open
192
Bernetti M, Hall KB, Bussi G. Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles. Nucleic Acids Res 2021;49:e84. [PMID: 34107023 PMCID: PMC8373061 DOI: 10.1093/nar/gkab459] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 01/03/2023]  Open
193
Using yeast two-hybrid system and molecular dynamics simulation to detect venom protein-protein interactions. Curr Res Toxicol 2021;2:93-98. [PMID: 34345854 PMCID: PMC8320608 DOI: 10.1016/j.crtox.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/14/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]  Open
194
Du XZ, Hua XF, Zhang ZY. Choice of force fields and water models for sampling solution conformations of bacteriophage T4 lysozyme. CHINESE J CHEM PHYS 2021. [DOI: 10.1063/1674-0068/cjcp2010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
195
Stark LE, Guan W, Colvin ME, LiWang PJ. The binding and specificity of chemokine binding proteins, through the lens of experiment and computation. Biomed J 2021;45:439-453. [PMID: 34311129 PMCID: PMC9421921 DOI: 10.1016/j.bj.2021.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 11/26/2022]  Open
196
Ohkubo YZ, Madsen JJ. Uncovering Membrane-Bound Models of Coagulation Factors by Combined Experimental and Computational Approaches. Thromb Haemost 2021;121:1122-1137. [PMID: 34214998 PMCID: PMC8432591 DOI: 10.1055/s-0040-1722187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
197
Justino GC, Nascimento CP, Justino MC. Molecular dynamics simulations and analysis for bioinformatics undergraduate students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021;49:570-582. [PMID: 33844418 DOI: 10.1002/bmb.21512] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 02/21/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
198
Andoh Y, Ichikawa SI, Sakashita T, Yoshii N, Okazaki S. Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations. J Comput Chem 2021;42:1073-1087. [PMID: 33780021 DOI: 10.1002/jcc.26524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
199
Callea L, Bonati L, Motta S. Metadynamics-Based Approaches for Modeling the Hypoxia-Inducible Factor 2α Ligand Binding Process. J Chem Theory Comput 2021;17:3841-3851. [PMID: 34082524 PMCID: PMC8280741 DOI: 10.1021/acs.jctc.1c00114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
200
Zhang L, Fleck NA. Molecular dynamics simulations of ultrathin PMMA films. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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