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For: Invernizzi M, Parrinello M. Exploration vs Convergence Speed in Adaptive-Bias Enhanced Sampling. J Chem Theory Comput 2022;18:3988-3996. [PMID: 35617155 PMCID: PMC9202311 DOI: 10.1021/acs.jctc.2c00152] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Ansari N, Jing ZF, Gagelin A, Hédin F, Aviat F, Hénin J, Piquemal JP, Lagardère L. Lambda-ABF-OPES: Faster Convergence with High Accuracy in Alchemical Free Energy Calculations. J Phys Chem Lett 2025;16:4626-4634. [PMID: 40312308 DOI: 10.1021/acs.jpclett.5c00683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2025]
2
Trizio E, Kang P, Parrinello M. Everything everywhere all at once: a probability-based enhanced sampling approach to rare events. NATURE COMPUTATIONAL SCIENCE 2025:10.1038/s43588-025-00799-5. [PMID: 40325221 DOI: 10.1038/s43588-025-00799-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2024] [Accepted: 04/02/2025] [Indexed: 05/07/2025]
3
Hanni J, Ray D. Data efficient learning of molecular slow modes from nonequilibrium metadynamics. J Chem Phys 2025;162:164101. [PMID: 40260824 DOI: 10.1063/5.0258483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2025] [Accepted: 04/03/2025] [Indexed: 04/24/2025]  Open
4
Devergne T, Kostic V, Pontil M, Parrinello M. Slow dynamical modes from static averages. J Chem Phys 2025;162:124108. [PMID: 40130793 DOI: 10.1063/5.0246248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Accepted: 03/02/2025] [Indexed: 03/26/2025]  Open
5
Tribello GA, Bonomi M, Bussi G, Camilloni C, Armstrong BI, Arsiccio A, Aureli S, Ballabio F, Bernetti M, Bonati L, Brookes SGH, Brotzakis ZF, Capelli R, Ceriotti M, Chan KT, Cossio P, Dasetty S, Donadio D, Ensing B, Ferguson AL, Fraux G, Gale JD, Gervasio FL, Giorgino T, Herringer NSM, Hocky GM, Hoff SE, Invernizzi M, Languin-Cattoën O, Leone V, Limongelli V, Lopez-Acevedo O, Marinelli F, Febrer Martinez P, Masetti M, Mehdi S, Michaelides A, Murtada MH, Parrinello M, Piaggi PM, Pietropaolo A, Pietrucci F, Pipolo S, Pritchard C, Raiteri P, Raniolo S, Rapetti D, Rizzi V, Rydzewski J, Salvalaglio M, Schran C, Seal A, Shayesteh Zadeh A, Silva TFD, Spiwok V, Stirnemann G, Sucerquia D, Tiwary P, Valsson O, Vendruscolo M, Voth GA, White AD, Wu J. PLUMED Tutorials: A collaborative, community-driven learning ecosystem. J Chem Phys 2025;162:092501. [PMID: 40035582 DOI: 10.1063/5.0251501] [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: 12/03/2024] [Accepted: 01/28/2025] [Indexed: 03/05/2025]  Open
6
Zlobin A, Maslova V, Beliaeva J, Meiler J, Golovin A. Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design. J Chem Inf Model 2025;65:2003-2013. [PMID: 39928564 PMCID: PMC11863386 DOI: 10.1021/acs.jcim.4c01827] [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: 10/05/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 02/12/2025]
7
Zhang P, Xu X. Propensity of Water Self-Ions at Air(Oil)-Water Interfaces Revealed by Deep Potential Molecular Dynamics with Enhanced Sampling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2025;41:3675-3683. [PMID: 39882949 DOI: 10.1021/acs.langmuir.4c05004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2025]
8
Bemelmans MP, Cournia Z, Damm-Ganamet KL, Gervasio FL, Pande V. Computational advances in discovering cryptic pockets for drug discovery. Curr Opin Struct Biol 2025;90:102975. [PMID: 39778412 DOI: 10.1016/j.sbi.2024.102975] [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: 09/14/2024] [Revised: 11/27/2024] [Accepted: 12/06/2024] [Indexed: 01/11/2025]
9
Church J, Blumer O, Keidar TD, Ploutno L, Reuveni S, Hirshberg B. Accelerating Molecular Dynamics through Informed Resetting. J Chem Theory Comput 2025;21:605-613. [PMID: 39772645 PMCID: PMC11781593 DOI: 10.1021/acs.jctc.4c01238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 12/20/2024] [Accepted: 12/23/2024] [Indexed: 01/11/2025]
10
Yang H, Raucci U, Iyer S, Hasan G, Golin Almeida T, Barua S, Savolainen A, Kangasluoma J, Rissanen M, Vehkamäki H, Kurtén T. Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis. Nat Commun 2025;16:661. [PMID: 39809821 PMCID: PMC11733028 DOI: 10.1038/s41467-025-55985-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 01/02/2025] [Indexed: 01/16/2025]  Open
11
Ray D, Rizzi V. Enhanced Sampling with Suboptimal Collective Variables: Reconciling Accuracy and Convergence Speed. J Chem Theory Comput 2025;21:58-69. [PMID: 39729052 DOI: 10.1021/acs.jctc.4c01231] [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: 12/28/2024]
12
Kim H, Pak Y. Free Energy-Based Refinement of DNA Force Field via Modification of Multiple Nonbonding Energy Terms. J Chem Inf Model 2025;65:288-297. [PMID: 39723478 DOI: 10.1021/acs.jcim.4c01918] [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: 12/28/2024]
13
Magsumov T, Ibraev I, Sedov I. Probing the Conformational Ensemble of the Amyloid Beta 16-22 Fragment with Parallel-Bias Metadynamics. J Phys Chem B 2024;128:12333-12347. [PMID: 39635892 DOI: 10.1021/acs.jpcb.4c04919] [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: 12/07/2024]
14
Glisman A, Mantha S, Yu D, Wasserman EP, Backer S, Reyes L, Wang ZG. Binding Modes and Water-Mediation of Polyelectrolyte Adsorption to a Neutral CaCO3 Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024;40:25931-25939. [PMID: 39620720 PMCID: PMC11636259 DOI: 10.1021/acs.langmuir.4c03301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 11/04/2024] [Accepted: 11/19/2024] [Indexed: 12/11/2024]
15
Febrer Martinez P, Rizzi V, Aureli S, Gervasio FL. Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol. J Chem Theory Comput 2024;20:10275-10287. [PMID: 39541508 PMCID: PMC11603614 DOI: 10.1021/acs.jctc.4c01112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 11/01/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
16
Aureli S, Bellina F, Rizzi V, Gervasio FL. Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study. J Chem Inf Model 2024;64:8595-8603. [PMID: 39526676 PMCID: PMC11600507 DOI: 10.1021/acs.jcim.4c01166] [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: 07/04/2024] [Revised: 10/23/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024]
17
Fu H, Zhou M, Chipot C, Cai W. Overcoming Sampling Issues and Improving Computational Efficiency in Collective-Variable-Based Enhanced-Sampling Simulations: A Tutorial. J Phys Chem B 2024;128:9706-9713. [PMID: 39321324 DOI: 10.1021/acs.jpcb.4c04857] [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]
18
Zhang M, Wu H, Wang Y. Enhanced Sampling of Biomolecular Slow Conformational Transitions Using Adaptive Sampling and Machine Learning. J Chem Theory Comput 2024;20:8569-8582. [PMID: 39301626 DOI: 10.1021/acs.jctc.4c00764] [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: 09/22/2024]
19
Das M, Venkatramani R. A Mode Evolution Metric to Extract Reaction Coordinates for Biomolecular Conformational Transitions. J Chem Theory Comput 2024;20:8422-8436. [PMID: 39287954 DOI: 10.1021/acs.jctc.4c00744] [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: 09/19/2024]
20
Karrenbrock M, Borsatto A, Rizzi V, Lukauskis D, Aureli S, Luigi Gervasio F. Absolute Binding Free Energies with OneOPES. J Phys Chem Lett 2024;15:9871-9880. [PMID: 39302888 PMCID: PMC11457222 DOI: 10.1021/acs.jpclett.4c02352] [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: 08/09/2024] [Revised: 09/13/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
21
Tiwari V, Bhattacharyya A, Karmakar T. A molecular dynamics study on the ion-mediated self-assembly of monolayer-protected nanoclusters. NANOSCALE 2024;16:15141-15147. [PMID: 39081010 DOI: 10.1039/d4nr02427c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
22
Salvadori G, Mennucci B. Analogies and Differences in the Photoactivation Mechanism of Bathy and Canonical Bacteriophytochromes Revealed by Multiscale Modeling. J Phys Chem Lett 2024;15:8078-8084. [PMID: 39087732 PMCID: PMC11376688 DOI: 10.1021/acs.jpclett.4c01823] [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: 08/02/2024]
23
Romagnoli A, Rexha J, Perta N, Di Cristofano S, Borgognoni N, Venturini G, Pignotti F, Raimondo D, Borsello T, Di Marino D. Peptidomimetics design and characterization: Bridging experimental and computer-based approaches. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024;212:279-327. [PMID: 40122649 DOI: 10.1016/bs.pmbts.2024.07.002] [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: 03/25/2025]
24
Hsu WT, Shirts MR. Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. J Chem Theory Comput 2024;20:6062-6081. [PMID: 39007702 PMCID: PMC11740319 DOI: 10.1021/acs.jctc.4c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
25
Mondal S, Karmakar T. Insights into the mechanism of peptide fibril growth on gold surface. Biophys Chem 2024;310:107237. [PMID: 38640598 DOI: 10.1016/j.bpc.2024.107237] [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: 01/23/2024] [Revised: 03/24/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
26
Kim H, Pak Y. Isomerization Pathways of a Mismatched Base Pair of A:8OG in Free Duplex DNA. J Chem Inf Model 2024;64:4511-4517. [PMID: 38767002 DOI: 10.1021/acs.jcim.4c00563] [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: 05/22/2024]
27
Blumer O, Reuveni S, Hirshberg B. Short-Time Infrequent Metadynamics for Improved Kinetics Inference. J Chem Theory Comput 2024;20:3484-3491. [PMID: 38668722 PMCID: PMC11099961 DOI: 10.1021/acs.jctc.4c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/15/2024]
28
Zhang P, Gardini AT, Xu X, Parrinello M. Intramolecular and Water Mediated Tautomerism of Solvated Glycine. J Chem Inf Model 2024;64:3599-3604. [PMID: 38620066 DOI: 10.1021/acs.jcim.4c00273] [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: 04/17/2024]
29
Borsatto A, Gianquinto E, Rizzi V, Gervasio FL. SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein-Protein Interfaces. J Chem Theory Comput 2024;20:3335-3348. [PMID: 38563746 PMCID: PMC11044271 DOI: 10.1021/acs.jctc.3c01318] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024]
30
Müllender L, Rizzi A, Parrinello M, Carloni P, Mandelli D. Effective data-driven collective variables for free energy calculations from metadynamics of paths. PNAS NEXUS 2024;3:pgae159. [PMID: 38665160 PMCID: PMC11044970 DOI: 10.1093/pnasnexus/pgae159] [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: 12/05/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
31
Kim H, Pak Y. Three-State Diffusion Model of DNA Glycosylase Translocation along Stretched DNA as Revealed by Free Energy Landscapes at the All-Atom Level. J Chem Theory Comput 2024;20:2666-2675. [PMID: 38451471 DOI: 10.1021/acs.jctc.4c00043] [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: 03/08/2024]
32
Ray D, Parrinello M. Data-driven classification of ligand unbinding pathways. Proc Natl Acad Sci U S A 2024;121:e2313542121. [PMID: 38412121 PMCID: PMC10927508 DOI: 10.1073/pnas.2313542121] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 01/26/2024] [Indexed: 02/29/2024]  Open
33
Yang M, Trizio E, Parrinello M. Structure and polymerization of liquid sulfur across the λ-transition. Chem Sci 2024;15:3382-3392. [PMID: 38425540 PMCID: PMC10902632 DOI: 10.1039/d3sc06282a] [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: 11/23/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024]  Open
34
Fu H, Bian H, Shao X, Cai W. Collective Variable-Based Enhanced Sampling: From Human Learning to Machine Learning. J Phys Chem Lett 2024;15:1774-1783. [PMID: 38329095 DOI: 10.1021/acs.jpclett.3c03542] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
35
Ruiz Munevar M, Rizzi V, Portioli C, Vidossich P, Cao E, Parrinello M, Cancedda L, De Vivo M. Cation Chloride Cotransporter NKCC1 Operates through a Rocking-Bundle Mechanism. J Am Chem Soc 2024;146:552-566. [PMID: 38146212 PMCID: PMC10786066 DOI: 10.1021/jacs.3c10258] [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: 09/18/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 12/27/2023]
36
Blumer O, Reuveni S, Hirshberg B. Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations. Nat Commun 2024;15:240. [PMID: 38172126 PMCID: PMC10764788 DOI: 10.1038/s41467-023-44528-w] [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: 08/09/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024]  Open
37
Fu H, Chipot C, Shao X, Cai W. Standard Binding Free-Energy Calculations: How Far Are We from Automation? J Phys Chem B 2023;127:10459-10468. [PMID: 37824848 DOI: 10.1021/acs.jpcb.3c04370] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
38
Bonati L, Polino D, Pizzolitto C, Biasi P, Eckert R, Reitmeier S, Schlögl R, Parrinello M. The role of dynamics in heterogeneous catalysis: Surface diffusivity and N2 decomposition on Fe(111). Proc Natl Acad Sci U S A 2023;120:e2313023120. [PMID: 38060558 PMCID: PMC10723053 DOI: 10.1073/pnas.2313023120] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/18/2023] [Indexed: 12/17/2023]  Open
39
Kim H, Kim E, Pak Y. Computational Probing of the Folding Mechanism of Human Telomeric G-Quadruplex DNA. J Chem Inf Model 2023;63:6366-6375. [PMID: 37782649 DOI: 10.1021/acs.jcim.3c01257] [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: 10/04/2023]
40
Pasarkar AP, Bencomo GM, Olsson S, Dieng AB. Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration. J Chem Phys 2023;159:144108. [PMID: 37823459 DOI: 10.1063/5.0166172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]  Open
41
Conflitti P, Raniolo S, Limongelli V. Perspectives on Ligand/Protein Binding Kinetics Simulations: Force Fields, Machine Learning, Sampling, and User-Friendliness. J Chem Theory Comput 2023;19:6047-6061. [PMID: 37656199 PMCID: PMC10536999 DOI: 10.1021/acs.jctc.3c00641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 09/02/2023]
42
Ray D, Parrinello M. Kinetics from Metadynamics: Principles, Applications, and Outlook. J Chem Theory Comput 2023;19:5649-5670. [PMID: 37585703 DOI: 10.1021/acs.jctc.3c00660] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
43
Rizzi V, Aureli S, Ansari N, Gervasio FL. OneOPES, a Combined Enhanced Sampling Method to Rule Them All. J Chem Theory Comput 2023;19:5731-5742. [PMID: 37603295 PMCID: PMC10500989 DOI: 10.1021/acs.jctc.3c00254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Indexed: 08/22/2023]
44
Tiwari V, Karmakar T. Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters. J Phys Chem Lett 2023:6686-6694. [PMID: 37463483 DOI: 10.1021/acs.jpclett.3c01770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
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Blazhynska M, Goulard Coderc de Lacam E, Chen H, Chipot C. Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning. J Chem Theory Comput 2023. [PMID: 37196198 DOI: 10.1021/acs.jctc.3c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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Hsu WT, Piomponi V, Merz PT, Bussi G, Shirts MR. Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. J Chem Theory Comput 2023;19:1805-1817. [PMID: 36853624 DOI: 10.1021/acs.jctc.2c01258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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Invernizzi M, Krämer A, Clementi C, Noé F. Skipping the Replica Exchange Ladder with Normalizing Flows. J Phys Chem Lett 2022;13:11643-11649. [PMID: 36484770 DOI: 10.1021/acs.jpclett.2c03327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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Enhancing sampling with free-energy calculations. Curr Opin Struct Biol 2022;77:102497. [PMID: 36410221 DOI: 10.1016/j.sbi.2022.102497] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022]
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Bal KM, Neyts EC. Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory. J Chem Phys 2022;157:184113. [DOI: 10.1063/5.0120136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
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Raucci U, Sanchez DM, Martínez TJ, Parrinello M. Enhanced Sampling Aided Design of Molecular Photoswitches. J Am Chem Soc 2022;144:19265-19271. [PMID: 36222799 DOI: 10.1021/jacs.2c04419] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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