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For: Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman GR. Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes. J Chem Theory Comput 2018;14:5459-5475. [PMID: 30240203 PMCID: PMC6571142 DOI: 10.1021/acs.jctc.8b00500] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Number Cited by Other Article(s)
1
Nadeem H, Shukla D. Ensemble Adaptive Sampling Scheme: Identifying an Optimal Sampling Strategy via Policy Ranking. J Chem Theory Comput 2025;21:4626-4639. [PMID: 40261689 DOI: 10.1021/acs.jctc.4c01488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2025]
2
Roessner RA, Floquet N, Louet M. Unveiling G-Protein-Coupled Receptor Conformational Dynamics via Metadynamics Simulations and Markov State Models. J Chem Inf Model 2025;65:4630-4642. [PMID: 40272908 DOI: 10.1021/acs.jcim.5c00202] [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: 04/26/2025]
3
El Ahdab D, Lagardère L, Hobaika Z, Jaffrelot Inizan T, Célerse F, Gresh N, Maroun RG, Piquemal JP. AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: From the c-Kit Proto-Oncogene to HIV-1. J Chem Inf Model 2025;65:4488-4500. [PMID: 40309760 DOI: 10.1021/acs.jcim.4c01680] [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: 05/02/2025]
4
Shen W, Wan K, Li D, Gao H, Shi X. Adaptive CVgen: Leveraging reinforcement learning for advanced sampling in protein folding and chemical reactions. Proc Natl Acad Sci U S A 2024;121:e2414205121. [PMID: 39475640 PMCID: PMC11551409 DOI: 10.1073/pnas.2414205121] [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: 07/15/2024] [Accepted: 09/24/2024] [Indexed: 11/13/2024]  Open
5
Dutta S, Zhao L, Shukla D. Dynamic Mechanism for Subtype Selectivity of Endocannabinoids. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.25.620304. [PMID: 39554065 PMCID: PMC11565827 DOI: 10.1101/2024.10.25.620304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
6
Roy A, Paul I, Luharuka S, Ray S. An in-silico scaffold- hopping approach to design novel inhibitors against gp130: A potential therapeutic application in cancer and Covid-19. Mol Divers 2024;28:3129-3151. [PMID: 37934366 DOI: 10.1007/s11030-023-10737-0] [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: 01/05/2023] [Accepted: 09/25/2023] [Indexed: 11/08/2023]
7
Gapsys V, Kopec W, Matthes D, de Groot BL. Biomolecular simulations at the exascale: From drug design to organelles and beyond. Curr Opin Struct Biol 2024;88:102887. [PMID: 39029280 DOI: 10.1016/j.sbi.2024.102887] [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: 12/24/2023] [Revised: 06/07/2024] [Accepted: 06/24/2024] [Indexed: 07/21/2024]
8
Fantasia A, Rovaris F, Abou El Kheir O, Marzegalli A, Lanzoni D, Pessina L, Xiao P, Zhou C, Li L, Henkelman G, Scalise E, Montalenti F. Development of a machine learning interatomic potential for exploring pressure-dependent kinetics of phase transitions in germanium. J Chem Phys 2024;161:014110. [PMID: 38953439 DOI: 10.1063/5.0214588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024]  Open
9
Marques S, Kouba P, Legrand A, Sedlar J, Disson L, Planas-Iglesias J, Sanusi Z, Kunka A, Damborsky J, Pajdla T, Prokop Z, Mazurenko S, Sivic J, Bednar D. CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS AU 2024;4:2228-2245. [PMID: 38938816 PMCID: PMC11200249 DOI: 10.1021/jacsau.4c00182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/24/2024] [Accepted: 05/13/2024] [Indexed: 06/29/2024]
10
Mehdi S, Smith Z, Herron L, Zou Z, Tiwary P. Enhanced Sampling with Machine Learning. Annu Rev Phys Chem 2024;75:347-370. [PMID: 38382572 PMCID: PMC11213683 DOI: 10.1146/annurev-physchem-083122-125941] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
11
Nguyen HH, Tufts J, Minh DDL. On Inactivation of the Coronavirus Main Protease. J Chem Inf Model 2024;64:1644-1656. [PMID: 38423522 PMCID: PMC10936523 DOI: 10.1021/acs.jcim.3c01518] [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: 10/05/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024]
12
Kozlowski N, Grubmüller H. Uncertainties in Markov State Models of Small Proteins. J Chem Theory Comput 2023;19:5516-5524. [PMID: 37540193 PMCID: PMC10448719 DOI: 10.1021/acs.jctc.3c00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Indexed: 08/05/2023]
13
Voelz VA, Pande VS, Bowman GR. Folding@home: Achievements from over 20 years of citizen science herald the exascale era. Biophys J 2023;122:2852-2863. [PMID: 36945779 PMCID: PMC10398258 DOI: 10.1016/j.bpj.2023.03.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/26/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]  Open
14
Qiu Y, O’Connor MS, Xue M, Liu B, Huang X. An Efficient Path Classification Algorithm Based on Variational Autoencoder to Identify Metastable Path Channels for Complex Conformational Changes. J Chem Theory Comput 2023;19:4728-4742. [PMID: 37382437 PMCID: PMC11042546 DOI: 10.1021/acs.jctc.3c00318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
15
Dutta S, Shukla D. Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Commun Biol 2023;6:485. [PMID: 37147497 PMCID: PMC10163236 DOI: 10.1038/s42003-023-04868-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/24/2023] [Indexed: 05/07/2023]  Open
16
Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. From Deep Mutational Mapping of Allosteric Protein Landscapes to Deep Learning of Allostery and Hidden Allosteric Sites: Zooming in on "Allosteric Intersection" of Biochemical and Big Data Approaches. Int J Mol Sci 2023;24:7747. [PMID: 37175454 PMCID: PMC10178073 DOI: 10.3390/ijms24097747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/22/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023]  Open
17
Meller A, De Oliveira S, Davtyan A, Abramyan T, Bowman GR, van den Bedem H. Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors. Front Mol Biosci 2023;10:1171143. [PMID: 37143823 PMCID: PMC10151774 DOI: 10.3389/fmolb.2023.1171143] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/07/2023] [Indexed: 05/06/2023]  Open
18
Agajanian S, Alshahrani M, Bai F, Tao P, Verkhivker GM. Exploring and Learning the Universe of Protein Allostery Using Artificial Intelligence Augmented Biophysical and Computational Approaches. J Chem Inf Model 2023;63:1413-1428. [PMID: 36827465 PMCID: PMC11162550 DOI: 10.1021/acs.jcim.2c01634] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
19
Tamadonfar KO, Di Venanzio G, Pinkner JS, Dodson KW, Kalas V, Zimmerman MI, Bazan Villicana J, Bowman GR, Feldman MF, Hultgren SJ. Structure-function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections. Proc Natl Acad Sci U S A 2023;120:e2212694120. [PMID: 36652481 PMCID: PMC9942807 DOI: 10.1073/pnas.2212694120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/17/2022] [Indexed: 01/19/2023]  Open
20
Lee LA, Barrick SK, Meller A, Walklate J, Lotthammer JM, Tay JW, Stump WT, Bowman G, Geeves MA, Greenberg MJ, Leinwand LA. Functional divergence of the sarcomeric myosin, MYH7b, supports species-specific biological roles. J Biol Chem 2022;299:102657. [PMID: 36334627 PMCID: PMC9800208 DOI: 10.1016/j.jbc.2022.102657] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/14/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022]  Open
21
Chang L, Mondal A, Perez A. Towards rational computational peptide design. FRONTIERS IN BIOINFORMATICS 2022;2:1046493. [PMID: 36338806 PMCID: PMC9634169 DOI: 10.3389/fbinf.2022.1046493] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]  Open
22
Westerlund AM, Sridhar A, Dahl L, Andersson A, Bodnar AY, Delemotte L. Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin. PLoS Comput Biol 2022;18:e1010583. [PMID: 36206305 PMCID: PMC9581412 DOI: 10.1371/journal.pcbi.1010583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 10/19/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022]  Open
23
Wieczór M, Genna V, Aranda J, Badia RM, Gelpí JL, Gapsys V, de Groot BL, Lindahl E, Municoy M, Hospital A, Orozco M. Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022;13:e1622. [PMID: 35935573 PMCID: PMC9347456 DOI: 10.1002/wcms.1622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
24
Dutta S, Selvam B, Shukla D. Distinct Binding Mechanisms for Allosteric Sodium Ion in Cannabinoid Receptors. ACS Chem Neurosci 2022;13:379-389. [PMID: 35019279 DOI: 10.1021/acschemneuro.1c00760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
25
Swanson JMJ. Multiscale kinetic analysis of proteins. Curr Opin Struct Biol 2022;72:169-175. [PMID: 34923310 PMCID: PMC9288830 DOI: 10.1016/j.sbi.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/30/2021] [Accepted: 11/01/2021] [Indexed: 02/03/2023]
26
Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling Profiles. ACS Pharmacol Transl Sci 2021;4:1543-1555. [PMID: 34661073 PMCID: PMC8506602 DOI: 10.1021/acsptsci.1c00095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 01/04/2023]
27
Markov state modeling of membrane transport proteins. J Struct Biol 2021;213:107800. [PMID: 34600140 DOI: 10.1016/j.jsb.2021.107800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/20/2021] [Accepted: 09/20/2021] [Indexed: 12/31/2022]
28
Konovalov K, Unarta IC, Cao S, Goonetilleke EC, Huang X. Markov State Models to Study the Functional Dynamics of Proteins in the Wake of Machine Learning. JACS AU 2021;1:1330-1341. [PMID: 34604842 PMCID: PMC8479766 DOI: 10.1021/jacsau.1c00254] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Indexed: 05/19/2023]
29
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophys J 2021;120:2880-2889. [PMID: 33794150 PMCID: PMC8007187 DOI: 10.1016/j.bpj.2021.03.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/17/2021] [Accepted: 03/25/2021] [Indexed: 01/12/2023]  Open
30
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nat Chem 2021;13:651-659. [PMID: 34031561 PMCID: PMC8249329 DOI: 10.1038/s41557-021-00707-0] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/14/2021] [Indexed: 01/20/2023]
31
Jaffrelot Inizan T, Célerse F, Adjoua O, El Ahdab D, Jolly LH, Liu C, Ren P, Montes M, Lagarde N, Lagardère L, Monmarché P, Piquemal JP. High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling. Chem Sci 2021;12:4889-4907. [PMID: 34168762 PMCID: PMC8179654 DOI: 10.1039/d1sc00145k] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 01/27/2021] [Indexed: 01/03/2023]  Open
32
Ge Y, Voelz VA. Markov State Models to Elucidate Ligand Binding Mechanism. Methods Mol Biol 2021;2266:239-259. [PMID: 33759131 DOI: 10.1007/978-1-0716-1209-5_14] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
33
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.10.420109. [PMID: 33330873 PMCID: PMC7743098 DOI: 10.1101/2020.12.10.420109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
34
Abella JR, Antunes D, Jackson K, Lizée G, Clementi C, Kavraki LE. Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes. Proc Natl Acad Sci U S A 2020;117:30610-30618. [PMID: 33184174 PMCID: PMC7720115 DOI: 10.1073/pnas.2007246117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
35
Hruska E, Balasubramanian V, Lee H, Jha S, Clementi C. Extensible and Scalable Adaptive Sampling on Supercomputers. J Chem Theory Comput 2020;16:7915-7925. [PMID: 33170696 DOI: 10.1021/acs.jctc.0c00991] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
36
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, Voelz VA, Chodera JD, Bowman GR. SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.27.175430. [PMID: 32637963 PMCID: PMC7337393 DOI: 10.1101/2020.06.27.175430] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
37
Yan S, Peck JM, Ilgu M, Nilsen-Hamilton M, Lamm MH. Sampling Performance of Multiple Independent Molecular Dynamics Simulations of an RNA Aptamer. ACS OMEGA 2020;5:20187-20201. [PMID: 32832772 PMCID: PMC7439393 DOI: 10.1021/acsomega.0c01867] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/22/2020] [Indexed: 06/11/2023]
38
Herrera-Nieto P, Pérez A, De Fabritiis G. Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. J Chem Inf Model 2020;60:5003-5010. [DOI: 10.1021/acs.jcim.0c00381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
39
Verkhivker GM, Agajanian S, Hu G, Tao P. Allosteric Regulation at the Crossroads of New Technologies: Multiscale Modeling, Networks, and Machine Learning. Front Mol Biosci 2020;7:136. [PMID: 32733918 PMCID: PMC7363947 DOI: 10.3389/fmolb.2020.00136] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]  Open
40
Pérez A, Herrera-Nieto P, Doerr S, De Fabritiis G. AdaptiveBandit: A Multi-armed Bandit Framework for Adaptive Sampling in Molecular Simulations. J Chem Theory Comput 2020;16:4685-4693. [DOI: 10.1021/acs.jctc.0c00205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
41
Porter JR, Meller A, Zimmerman MI, Greenberg MJ, Bowman GR. Conformational distributions of isolated myosin motor domains encode their mechanochemical properties. eLife 2020;9:e55132. [PMID: 32479265 PMCID: PMC7259954 DOI: 10.7554/elife.55132] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/04/2020] [Indexed: 01/25/2023]  Open
42
Yuan Y, Zhu Q, Song R, Ma J, Dong H. A Two-Ended Data-Driven Accelerated Sampling Method for Exploring the Transition Pathways between Two Known States of Protein. J Chem Theory Comput 2020;16:4631-4640. [PMID: 32320614 DOI: 10.1021/acs.jctc.9b01184] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Kells A, Koskin V, Rosta E, Annibale A. Correlation functions, mean first passage times, and the Kemeny constant. J Chem Phys 2020;152:104108. [PMID: 32171226 DOI: 10.1063/1.5143504] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
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Wan H, Voelz VA. Adaptive Markov state model estimation using short reseeding trajectories. J Chem Phys 2020;152:024103. [PMID: 31941308 DOI: 10.1063/1.5142457] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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Wang W, Shin WJ, Zhang B, Choi Y, Yoo JS, Zimmerman MI, Frederick TE, Bowman GR, Gross ML, Leung DW, Jung JU, Amarasinghe GK. The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target. Cell Rep 2020;30:153-163.e5. [PMID: 31914382 PMCID: PMC7214099 DOI: 10.1016/j.celrep.2019.12.020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 10/31/2019] [Accepted: 12/06/2019] [Indexed: 01/08/2023]  Open
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Sun Z, Wakefield AE, Kolossvary I, Beglov D, Vajda S. Structure-Based Analysis of Cryptic-Site Opening. Structure 2019;28:223-235.e2. [PMID: 31810712 DOI: 10.1016/j.str.2019.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 09/10/2019] [Accepted: 11/12/2019] [Indexed: 01/07/2023]
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Orellana L. Large-Scale Conformational Changes and Protein Function: Breaking the in silico Barrier. Front Mol Biosci 2019;6:117. [PMID: 31750315 PMCID: PMC6848229 DOI: 10.3389/fmolb.2019.00117] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022]  Open
48
Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, Jiang H, Chen K, Skene RJ, Zheng YG, Brown PJ, Jin J, Luo C, Chodera JD, Luo M. The dynamic conformational landscape of the protein methyltransferase SETD8. eLife 2019;8:45403. [PMID: 31081496 PMCID: PMC6579520 DOI: 10.7554/elife.45403] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/08/2019] [Indexed: 12/27/2022]  Open
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Kahana A, Lancet D. Protobiotic Systems Chemistry Analyzed by Molecular Dynamics. Life (Basel) 2019;9:E38. [PMID: 31083329 PMCID: PMC6617412 DOI: 10.3390/life9020038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022]  Open
50
Porter JR, Zimmerman MI, Bowman GR. Enspara: Modeling molecular ensembles with scalable data structures and parallel computing. J Chem Phys 2019;150:044108. [PMID: 30709308 DOI: 10.1063/1.5063794] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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