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For: Ansari N, Rizzi V, Parrinello M. Water regulates the residence time of Benzamidine in Trypsin. Nat Commun 2022;13:5438. [PMID: 36114175 PMCID: PMC9481606 DOI: 10.1038/s41467-022-33104-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/01/2022] [Indexed: 12/11/2022]  Open
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
Koch F, Jäger M, Tänzel V, Wolf S, Schilling T. Trust the force, but pull wisely: Structural insights into non-equilibrium response forces from pulling MD simulations. J Chem Phys 2025;162:144903. [PMID: 40202145 DOI: 10.1063/5.0254257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2024] [Accepted: 03/22/2025] [Indexed: 04/10/2025]  Open
3
Serra E, Ghidini A, Decherchi S, Cavalli A. Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation. J Chem Theory Comput 2025;21:2079-2094. [PMID: 39907631 DOI: 10.1021/acs.jctc.4c01453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2025]
4
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]
5
Kumari N, Sonam, Karmakar T. Enhanced Sampling Simulations of RNA-Peptide Binding Using Deep Learning Collective Variables. J Chem Inf Model 2025;65:563-570. [PMID: 39772512 DOI: 10.1021/acs.jcim.4c01438] [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: 01/11/2025]
6
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]
7
Zhang J, Bonati L, Trizio E, Zhang O, Kang Y, Hou T, Parrinello M. Descriptor-Free Collective Variables from Geometric Graph Neural Networks. J Chem Theory Comput 2024;20:10787-10797. [PMID: 39665183 DOI: 10.1021/acs.jctc.4c01197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
8
Zhou Y, Xu H, Xia T, Xiong L, Chang LC, Chang FJ, Xu CY. Methane degassing in global river reservoirs and its impacts on carbon budgets and sustainable water management. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024;957:177623. [PMID: 39579887 DOI: 10.1016/j.scitotenv.2024.177623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 10/27/2024] [Accepted: 11/16/2024] [Indexed: 11/25/2024]
9
Das S, Raucci U, Neves RPP, Ramos MJ, Parrinello M. Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables. Proc Natl Acad Sci U S A 2024;121:e2416621121. [PMID: 39589882 PMCID: PMC11626191 DOI: 10.1073/pnas.2416621121] [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: 08/15/2024] [Accepted: 10/27/2024] [Indexed: 11/28/2024]  Open
10
Zhao YQ, Li ZP, Dong SC, Wang H, Zhao YM, Dong LY, Zhao ZY, Wang XH. Preparation of micron-sized benzamidine-modified magnetic agarose beads for trypsin purification from fish viscera. Talanta 2024;280:126745. [PMID: 39180874 DOI: 10.1016/j.talanta.2024.126745] [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: 02/05/2024] [Revised: 07/09/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
11
Ojha AA, Votapka LW, Amaro RE. Advances and Challenges in Milestoning Simulations for Drug-Target Kinetics. J Chem Theory Comput 2024;20:9759-9769. [PMID: 39508322 PMCID: PMC11603602 DOI: 10.1021/acs.jctc.4c01108] [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: 09/06/2024] [Revised: 10/30/2024] [Accepted: 10/31/2024] [Indexed: 11/15/2024]
12
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]
13
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]
14
Wang M, Meng Y, Sajid M, Xie Z, Tong P, Ma Z, Zhang K, Shen D, Luo R, Song L, Wu L, Zheng X, Li X, Chen W. Bidentate Coordination Structure Facilitates High-Voltage and High-Utilization Aqueous Zn-I2 Batteries. Angew Chem Int Ed Engl 2024;63:e202404784. [PMID: 38868978 DOI: 10.1002/anie.202404784] [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: 03/09/2024] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
15
Sarkar D, Surpeta B, Brezovsky J. Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites. J Chem Theory Comput 2024;20:5807-5819. [PMID: 38978395 PMCID: PMC11270739 DOI: 10.1021/acs.jctc.4c00452] [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: 04/05/2024] [Revised: 06/26/2024] [Accepted: 07/01/2024] [Indexed: 07/10/2024]
16
Aho N, Groenhof G, Buslaev P. Do All Paths Lead to Rome? How Reliable is Umbrella Sampling Along a Single Path? J Chem Theory Comput 2024. [PMID: 39039621 DOI: 10.1021/acs.jctc.4c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
17
Majumder A, Straub JE. Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane. J Chem Theory Comput 2024;20:5774-5783. [PMID: 38918177 PMCID: PMC11575465 DOI: 10.1021/acs.jctc.4c00454] [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] [Indexed: 06/27/2024]
18
Muscat S, Errico S, Danani A, Chiti F, Grasso G. Leveraging Machine Learning-Guided Molecular Simulations Coupled with Experimental Data to Decipher Membrane Binding Mechanisms of Aminosterols. J Chem Theory Comput 2024. [PMID: 38979909 PMCID: PMC11447954 DOI: 10.1021/acs.jctc.4c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
19
Higuchi Y, Saleh MA, Anada T, Tanaka M, Hishida M. Rotational Dynamics of Water near Osmolytes by Molecular Dynamics Simulations. J Phys Chem B 2024;128:5008-5017. [PMID: 38728154 DOI: 10.1021/acs.jpcb.3c08470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
20
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
21
Beyerle ER, Tiwary P. Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation. J Phys Chem B 2024;128:755-767. [PMID: 38205806 DOI: 10.1021/acs.jpcb.3c08304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
22
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]
23
Chen J, Wang W, Sun H, He W. Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters. Mini Rev Med Chem 2024;24:1323-1333. [PMID: 38265367 DOI: 10.2174/0113895575252165231122095555] [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: 03/06/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 01/25/2024]
24
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]
25
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]
26
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]
27
Buigues P, Gehrke S, Badaoui M, Dudas B, Mandana G, Qi T, Bottegoni G, Rosta E. Investigating the Unbinding of Muscarinic Antagonists from the Muscarinic 3 Receptor. J Chem Theory Comput 2023;19:5260-5272. [PMID: 37458730 PMCID: PMC10413856 DOI: 10.1021/acs.jctc.3c00023] [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: 01/17/2023] [Indexed: 08/09/2023]
28
Hammerschmidt SJ, Maus H, Weldert AC, Gütschow M, Kersten C. Improving binding entropy by higher ligand symmetry? - A case study with human matriptase. RSC Med Chem 2023;14:969-982. [PMID: 37252099 PMCID: PMC10211324 DOI: 10.1039/d3md00125c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023]  Open
29
Wolf S. Predicting Protein-Ligand Binding and Unbinding Kinetics with Biased MD Simulations and Coarse-Graining of Dynamics: Current State and Challenges. J Chem Inf Model 2023;63:2902-2910. [PMID: 37133392 DOI: 10.1021/acs.jcim.3c00151] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
30
Wang J, Do HN, Koirala K, Miao Y. Predicting Biomolecular Binding Kinetics: A Review. J Chem Theory Comput 2023;19:2135-2148. [PMID: 36989090 DOI: 10.1021/acs.jctc.2c01085] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
31
Sohraby F, Nunes-Alves A. Advances in computational methods for ligand binding kinetics. Trends Biochem Sci 2022;48:437-449. [PMID: 36566088 DOI: 10.1016/j.tibs.2022.11.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
32
Kinetics of Drug Release from Clay Using Enhanced Sampling Methods. Pharmaceutics 2022;14:pharmaceutics14122586. [PMID: 36559081 PMCID: PMC9781022 DOI: 10.3390/pharmaceutics14122586] [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: 10/14/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]  Open
33
Ray D, Ansari N, Rizzi V, Invernizzi M, Parrinello M. Rare Event Kinetics from Adaptive Bias Enhanced Sampling. J Chem Theory Comput 2022;18:6500-6509. [PMID: 36194840 DOI: 10.1021/acs.jctc.2c00806] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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