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For: Song LF, Merz KM. Evolution of Alchemical Free Energy Methods in Drug Discovery. J Chem Inf Model 2020;60:5308-5318. [DOI: 10.1021/acs.jcim.0c00547] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Martínez-Ortega U, Aguayo-Ortiz R, Aguilar-Cazares D, Guerrero-Molina ED, Aguilar-Martínez V, Moreno-Rodríguez A, López-González JS, Vázquez-Ramos JM, Hernández-Luis F. Alchemical free energy-based optimization of quinazoline derivatives as potent EGFR inhibitors with cytotoxic activity. Bioorg Med Chem 2025;124:118179. [PMID: 40199186 DOI: 10.1016/j.bmc.2025.118179] [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: 01/17/2025] [Revised: 03/27/2025] [Accepted: 03/30/2025] [Indexed: 04/10/2025]
2
Koby SB, Gutkin E, Patel S, Kurnikova MG. Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations. J Chem Inf Model 2025;65:4932-4951. [PMID: 40328725 PMCID: PMC12121625 DOI: 10.1021/acs.jcim.4c02107] [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: 01/06/2025] [Revised: 03/13/2025] [Accepted: 04/02/2025] [Indexed: 05/08/2025]
3
Gkeka P, Svensson F, Magadán CR, de Groot MJ, Jerome SV. Computational Hit Finding: An Industry Perspective. J Med Chem 2025. [PMID: 40392533 DOI: 10.1021/acs.jmedchem.4c03087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2025]
4
Laracuente X, Delfing BM, Luo X, Olson A, Jeffries W, Bowers SR, Foreman KW, Lee KH, Paige M, Kehn-Hall K, Lockhart C, Klimov DK. Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands. J Chem Theory Comput 2025;21:4286-4298. [PMID: 40189800 PMCID: PMC12020361 DOI: 10.1021/acs.jctc.5c00121] [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: 04/23/2025]
5
Liu R, Yao Y, Huang W, Zhong Y, Luo HB, Li Z. Divide-and-Conquer ABFE: Improving Free Energy Calculations by Enhancing Water Sampling. J Chem Theory Comput 2025;21:3712-3725. [PMID: 40127297 DOI: 10.1021/acs.jctc.4c01661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2025]
6
Zhou H, Fu H, Shao X, Cai W. Identification of novel inhibitors for epidermal growth factor receptor tyrosine kinase using absolute binding free-energy simulations. Int J Biol Macromol 2025;304:140989. [PMID: 39952524 DOI: 10.1016/j.ijbiomac.2025.140989] [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: 11/26/2024] [Revised: 01/16/2025] [Accepted: 02/11/2025] [Indexed: 02/17/2025]
7
Li P, Pu T, Mei Y. FEP-SPell-ABFE: An Open-Source Automated Alchemical Absolute Binding Free-Energy Calculation Workflow for Drug Discovery. J Chem Inf Model 2025;65:2711-2721. [PMID: 40029615 DOI: 10.1021/acs.jcim.4c01986] [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: 03/05/2025]
8
Tayfuroglu O, Zengin IN, Koca MS, Kocak A. DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations. J Chem Inf Model 2025;65:2818-2833. [PMID: 40033575 PMCID: PMC11938341 DOI: 10.1021/acs.jcim.4c02053] [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: 11/08/2024] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/05/2025]
9
Angelo M, Zhang W, Vilseck J, Aoki S. In silico λ-dynamics predicts protein binding specificities to modified RNAs. Nucleic Acids Res 2025;53:gkaf166. [PMID: 40066880 PMCID: PMC11894534 DOI: 10.1093/nar/gkaf166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/19/2025] [Accepted: 02/20/2025] [Indexed: 03/15/2025]  Open
10
Zheng T, Wang A, Han X, Xia Y, Xu X, Zhan J, Liu Y, Chen Y, Wang Z, Wu X, Gong S, Yan W. Data-driven parametrization of molecular mechanics force fields for expansive chemical space coverage. Chem Sci 2025;16:2730-2740. [PMID: 39802691 PMCID: PMC11721737 DOI: 10.1039/d4sc06640e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 12/25/2024] [Indexed: 01/16/2025]  Open
11
Furui K, Shimizu T, Akiyama Y, Kimura SR, Terada Y, Ohue M. PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Compound Transformations. J Chem Inf Model 2025;65:705-721. [PMID: 39800967 PMCID: PMC11776053 DOI: 10.1021/acs.jcim.4c01634] [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: 09/08/2024] [Revised: 12/19/2024] [Accepted: 12/23/2024] [Indexed: 01/28/2025]
12
Zhang S, Xie W, Yang Z, Xu S, Zhao Q, Lu Y, Zhang K, Yan Z, Chen J. Revealing the dissolution mechanism of organic carbonyl electrodes in lithium-organic batteries. Chem Sci 2025:d4sc07932a. [PMID: 39911342 PMCID: PMC11792205 DOI: 10.1039/d4sc07932a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2024] [Accepted: 01/23/2025] [Indexed: 02/07/2025]  Open
13
Bhati A, Wan S, Coveney PV. Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations. J Chem Theory Comput 2025;21:440-462. [PMID: 39680850 PMCID: PMC11736689 DOI: 10.1021/acs.jctc.4c01389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 11/28/2024] [Accepted: 12/02/2024] [Indexed: 12/18/2024]
14
Friedman AJ, Hsu WT, Shirts MR. Multiple Topology Replica Exchange of Expanded Ensembles for Multidimensional Alchemical Calculations. J Chem Theory Comput 2025;21:230-240. [PMID: 39743749 PMCID: PMC11732712 DOI: 10.1021/acs.jctc.4c01268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
15
Zhang BW, Fajer M, Chen W, Moraca F, Wang L. Leveraging the Thermodynamics of Protein Conformations in Drug Discovery. J Chem Inf Model 2025;65:252-264. [PMID: 39681511 DOI: 10.1021/acs.jcim.4c01612] [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: 12/18/2024]
16
Liesen M, Vilseck JZ. Superimposing Ligands with a Ligand Overlay as an Alternate Topology Model for λ-Dynamics-Based Calculations. J Phys Chem B 2024;128:11359-11368. [PMID: 39515788 PMCID: PMC11587946 DOI: 10.1021/acs.jpcb.4c04805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 10/10/2024] [Accepted: 10/15/2024] [Indexed: 11/16/2024]
17
Molani F, Cho AE. Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima. Commun Chem 2024;7:247. [PMID: 39468282 PMCID: PMC11519471 DOI: 10.1038/s42004-024-01328-7] [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: 06/15/2024] [Accepted: 10/14/2024] [Indexed: 10/30/2024]  Open
18
Musleh S, Alibay I, Biggin PC, Bryce RA. Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations. J Chem Inf Model 2024;64:8063-8073. [PMID: 39413277 PMCID: PMC11523069 DOI: 10.1021/acs.jcim.4c01088] [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: 06/25/2024] [Revised: 10/03/2024] [Accepted: 10/03/2024] [Indexed: 10/18/2024]
19
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]
20
Min Y, Wei Y, Wang P, Wang X, Li H, Wu N, Bauer S, Zheng S, Shi Y, Wang Y, Wu J, Zhao D, Zeng J. From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2405404. [PMID: 39206846 PMCID: PMC11516055 DOI: 10.1002/advs.202405404] [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: 05/17/2024] [Revised: 07/29/2024] [Indexed: 09/04/2024]
21
Pala D, Clark DE. Caught between a ROCK and a hard place: current challenges in structure-based drug design. Drug Discov Today 2024;29:104106. [PMID: 39029868 DOI: 10.1016/j.drudis.2024.104106] [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: 04/11/2024] [Revised: 06/27/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
22
Tan S, Gong X, Liu H, Yao X. Identification of novel LRRK2 inhibitors by structure-based virtual screening and alchemical free energy calculation. Phys Chem Chem Phys 2024;26:19775-19786. [PMID: 38984923 DOI: 10.1039/d4cp01762e] [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: 07/11/2024]
23
Lagardère L, Maurin L, Adjoua O, El Hage K, Monmarché P, Piquemal JP, Hénin J. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation. J Chem Theory Comput 2024;20:4481-4498. [PMID: 38805379 DOI: 10.1021/acs.jctc.3c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
24
Zhang S, Giese TJ, Lee TS, York DM. Alchemical Enhanced Sampling with Optimized Phase Space Overlap. J Chem Theory Comput 2024;20:3935-3953. [PMID: 38666430 PMCID: PMC11157682 DOI: 10.1021/acs.jctc.4c00251] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
25
Chéron N. Binding Sites of Bicarbonate in Phosphoenolpyruvate Carboxylase. J Chem Inf Model 2024;64:3375-3385. [PMID: 38533570 DOI: 10.1021/acs.jcim.3c01830] [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: 03/28/2024]
26
Cournia Z, Chipot C. Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. J Phys Chem B 2024;128:3299-3301. [PMID: 38600851 DOI: 10.1021/acs.jpcb.4c01283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
27
Cournia Z, Chipot C. Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. J Chem Inf Model 2024;64:2129-2131. [PMID: 38587007 DOI: 10.1021/acs.jcim.4c00349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
28
Luo D, Liu D, Qu X, Dong L, Wang B. Enhancing Generalizability in Protein-Ligand Binding Affinity Prediction with Multimodal Contrastive Learning. J Chem Inf Model 2024;64:1892-1906. [PMID: 38441880 DOI: 10.1021/acs.jcim.3c01961] [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: 03/26/2024]
29
Ries B, Alibay I, Swenson DWH, Baumann HM, Henry MM, Eastwood JRB, Gowers RJ. Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations. J Chem Theory Comput 2024;20:1862-1877. [PMID: 38330251 PMCID: PMC10941767 DOI: 10.1021/acs.jctc.3c01206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 02/10/2024]
30
Beck TL, Carloni P, Asthagiri DN. All-Atom Biomolecular Simulation in the Exascale Era. J Chem Theory Comput 2024;20:1777-1782. [PMID: 38382017 DOI: 10.1021/acs.jctc.3c01276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
31
Smith MD, Darryl Quarles L, Demerdash O, Smith JC. Drugging the entire human proteome: Are we there yet? Drug Discov Today 2024;29:103891. [PMID: 38246414 DOI: 10.1016/j.drudis.2024.103891] [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: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
32
Wu N, Zhang R, Peng X, Fang L, Chen K, Jestilä JS. Elucidation of protein-ligand interactions by multiple trajectory analysis methods. Phys Chem Chem Phys 2024;26:6903-6915. [PMID: 38334015 DOI: 10.1039/d3cp03492e] [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: 02/10/2024]
33
Zhou M, Zhao F, Yu L, Liu J, Wang J, Zhang JZH. An Efficient Approach to the Accurate Prediction of Mutational Effects in Antigen Binding to the MHC1. Molecules 2024;29:881. [PMID: 38398632 PMCID: PMC10892774 DOI: 10.3390/molecules29040881] [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: 12/25/2023] [Revised: 02/07/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]  Open
34
Hu R, Zhang J, Kang Y, Wang Z, Pan P, Deng Y, Hsieh CY, Hou T. Comprehensive, Open-Source, and Automated Workflow for Multisite λ-Dynamics in Lead Optimization. J Chem Theory Comput 2024;20:1465-1478. [PMID: 38300792 DOI: 10.1021/acs.jctc.3c01154] [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: 02/03/2024]
35
Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024;35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
36
Angelo M, Zhang W, Vilseck JZ, Aoki ST. In silico λ-dynamics predicts protein binding specificities to modified RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577511. [PMID: 38328125 PMCID: PMC10849657 DOI: 10.1101/2024.01.26.577511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
37
Herz AM, Kellici T, Morao I, Michel J. Alchemical Free Energy Workflows for the Computation of Protein-Ligand Binding Affinities. Methods Mol Biol 2024;2716:241-264. [PMID: 37702943 DOI: 10.1007/978-1-0716-3449-3_11] [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: 09/14/2023]
38
Robo MT, Hayes RL, Ding X, Pulawski B, Vilseck JZ. Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling. Nat Commun 2023;14:8515. [PMID: 38129400 PMCID: PMC10740020 DOI: 10.1038/s41467-023-44208-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/04/2023] [Indexed: 12/23/2023]  Open
39
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]
40
York DM. Modern Alchemical Free Energy Methods for Drug Discovery Explained. ACS PHYSICAL CHEMISTRY AU 2023;3:478-491. [PMID: 38034038 PMCID: PMC10683484 DOI: 10.1021/acsphyschemau.3c00033] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 12/02/2023]
41
Case D, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, Lee TS, Li P, Liu J, Luchko T, Luo R, Manathunga M, Machado MR, Nguyen HM, O’Hearn KA, Onufriev AV, Pan F, Pantano S, Qi R, Rahnamoun A, Risheh A, Schott-Verdugo S, Shajan A, Swails J, Wang J, Wei H, Wu X, Wu Y, Zhang S, Zhao S, Zhu Q, Cheatham TE, Roe DR, Roitberg A, Simmerling C, York DM, Nagan MC, Merz KM. AmberTools. J Chem Inf Model 2023;63:6183-6191. [PMID: 37805934 PMCID: PMC10598796 DOI: 10.1021/acs.jcim.3c01153] [Citation(s) in RCA: 573] [Impact Index Per Article: 286.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/10/2023]
42
Gracia Carmona O, Oostenbrink C. Flexible Gaussian Accelerated Molecular Dynamics to Enhance Biological Sampling. J Chem Theory Comput 2023;19:6521-6531. [PMID: 37649349 PMCID: PMC10536968 DOI: 10.1021/acs.jctc.3c00619] [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: 06/09/2023] [Indexed: 09/01/2023]
43
Lapierre J, Hub JS. Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy. J Chem Inf Model 2023;63:5319-5330. [PMID: 37560945 DOI: 10.1021/acs.jcim.3c00880] [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: 08/11/2023]
44
Lockhart C, Luo X, Olson A, Delfing BM, Laracuente XE, Foreman KW, Paige M, Kehn-Hall K, Klimov DK. Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites? J Chem Inf Model 2023;63:4791-4802. [PMID: 37531558 PMCID: PMC10947611 DOI: 10.1021/acs.jcim.3c00631] [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: 08/04/2023]
45
Jiang W. Enhanced Configurational Sampling Approaches to Alchemical Ligand Binding Free Energy Simulations: Current Status and Challenges. J Phys Chem B 2023;127:6835-6841. [PMID: 37499215 DOI: 10.1021/acs.jpcb.3c02020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
46
Sheng Z, Bimela JS, Wang M, Li Z, Guo Y, Ho DD. An optimized thermodynamics integration protocol for identifying beneficial mutations in antibody design. Front Immunol 2023;14:1190416. [PMID: 37275896 PMCID: PMC10235760 DOI: 10.3389/fimmu.2023.1190416] [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: 03/20/2023] [Accepted: 04/28/2023] [Indexed: 06/07/2023]  Open
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Gracia Carmona O, Gillhofer M, Tomasiak L, De Ruiter A, Oostenbrink C. Accelerated Enveloping Distribution Sampling to Probe the Presence of Water Molecules. J Chem Theory Comput 2023. [PMID: 37167545 DOI: 10.1021/acs.jctc.3c00109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
48
Morado J, Mortenson PN, Nissink JWM, Essex JW, Skylaris CK. Does a Machine-Learned Potential Perform Better Than an Optimally Tuned Traditional Force Field? A Case Study on Fluorohydrins. J Chem Inf Model 2023;63:2810-2827. [PMID: 37071825 PMCID: PMC10170518 DOI: 10.1021/acs.jcim.2c01510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
49
Del ng BM, Olson A, Laracuente XE, Foreman KW, Paige M, Kehn-Hall K, Lockhart C, Klimov DK. Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-α Receptors Explored with All-Atom Replica Exchange Molecular Dynamics. J Phys Chem B 2023;127:3175-3186. [PMID: 37001021 PMCID: PMC10358320 DOI: 10.1021/acs.jpcb.3c00429] [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: 04/03/2023]
50
Muegge I, Hu Y. Recent Advances in Alchemical Binding Free Energy Calculations for Drug Discovery. ACS Med Chem Lett 2023;14:244-250. [PMID: 36923913 PMCID: PMC10009785 DOI: 10.1021/acsmedchemlett.2c00541] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/07/2023] [Indexed: 02/18/2023]  Open
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