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For: Merski M, Fischer M, Balius TE, Eidam O, Shoichet BK. Homologous ligands accommodated by discrete conformations of a buried cavity. Proc Natl Acad Sci U S A 2015;112:5039-44. [PMID: 25847998 DOI: 10.1073/pnas.1500806112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
Number Cited by Other Article(s)
1
Smith L, Novak B, Osato M, Mobley DL, Bowman GR. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model. J Chem Theory Comput 2024;20:1036-1050. [PMID: 38291966 PMCID: PMC10867841 DOI: 10.1021/acs.jctc.3c00870] [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: 08/08/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 02/01/2024]
2
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PopShift: A thermodynamically sound approach to estimate binding free energies by accounting for ligand-induced population shifts from a ligand-free MSM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549110. [PMID: 37503302 PMCID: PMC10370083 DOI: 10.1101/2023.07.14.549110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
3
Ligand binding free energy evaluation by Monte Carlo Recursion. Comput Biol Chem 2023;103:107830. [PMID: 36812825 DOI: 10.1016/j.compbiolchem.2023.107830] [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: 11/22/2022] [Revised: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
4
Gracia Carmona O, Oostenbrink C. Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. J Chem Inf Model 2023;63:197-207. [PMID: 36512416 PMCID: PMC9832482 DOI: 10.1021/acs.jcim.2c01272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
5
Stachowski TR, Fischer M. Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots. J Med Chem 2022;65:13692-13704. [PMID: 35970514 PMCID: PMC9619398 DOI: 10.1021/acs.jmedchem.2c00708] [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] [Indexed: 11/30/2022]
6
Zhu S. Computational characterization of homologous ligands binding to a deep hydrophobic pocket in Shigella flexneri pilot protein MxiM. Proteins 2022;90:2116-2123. [DOI: 10.1002/prot.26402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/10/2022] [Accepted: 07/19/2022] [Indexed: 11/07/2022]
7
Reif MM, Zacharias M. Improving the Potential of Mean Force and Nonequilibrium Pulling Simulations by Simultaneous Alchemical Modifications. J Chem Theory Comput 2022;18:3873-3893. [PMID: 35653503 DOI: 10.1021/acs.jctc.1c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Tze-Yang Ng J, Tan YS. Accelerated Ligand-Mapping Molecular Dynamics Simulations for the Detection of Recalcitrant Cryptic Pockets and Occluded Binding Sites. J Chem Theory Comput 2022;18:1969-1981. [PMID: 35175753 DOI: 10.1021/acs.jctc.1c01177] [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]
9
Barletta GP, Barletta M, Saldaño TE, Fernandez-Alberti S. Analysis of changes of cavity volumes in predefined directions of protein motions and cavity flexibility. J Comput Chem 2021;43:391-401. [PMID: 34962296 DOI: 10.1002/jcc.26799] [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: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022]
10
Wu Y, Brooks CL. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. J Chem Inf Model 2021;61:5535-5549. [PMID: 34704754 PMCID: PMC8684595 DOI: 10.1021/acs.jcim.1c01078] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
11
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: 14] [Impact Index Per Article: 4.7] [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
12
Bradford SYC, El Khoury L, Ge Y, Osato M, Mobley DL, Fischer M. Temperature artifacts in protein structures bias ligand-binding predictions. Chem Sci 2021;12:11275-11293. [PMID: 34667539 PMCID: PMC8447925 DOI: 10.1039/d1sc02751d] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022]  Open
13
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Commun Chem 2021;4:61. [PMID: 36697634 PMCID: PMC9814727 DOI: 10.1038/s42004-021-00498-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 03/24/2021] [Indexed: 01/28/2023]  Open
14
Stein RM, Yang Y, Balius TE, O'Meara MJ, Lyu J, Young J, Tang K, Shoichet BK, Irwin JJ. Property-Unmatched Decoys in Docking Benchmarks. J Chem Inf Model 2021;61:699-714. [PMID: 33494610 DOI: 10.1021/acs.jcim.0c00598] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
15
Merski M, Skrzeczkowski J, Roth JK, Górna MW. A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins. Molecules 2020;25:E5326. [PMID: 33203097 PMCID: PMC7696500 DOI: 10.3390/molecules25225326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/08/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022]  Open
16
Protein-ligand binding with the coarse-grained Martini model. Nat Commun 2020;11:3714. [PMID: 32709852 PMCID: PMC7382508 DOI: 10.1038/s41467-020-17437-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 06/29/2020] [Indexed: 02/06/2023]  Open
17
Pal RK, Gallicchio E. Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations. J Chem Phys 2019;151:124116. [DOI: 10.1063/1.5123154] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
18
Niitsu A, Re S, Oshima H, Kamiya M, Sugita Y. De Novo Prediction of Binders and Nonbinders for T4 Lysozyme by gREST Simulations. J Chem Inf Model 2019;59:3879-3888. [DOI: 10.1021/acs.jcim.9b00416] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
19
Liu Y, Liu SY. Exploring the strength of a hydrogen bond as a function of steric environment using 1,2-azaborine ligands and engineered T4 lysozyme receptors. Org Biomol Chem 2019;17:7002-7006. [PMID: 31309207 DOI: 10.1039/c9ob01008d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
20
Nunes-Alves A, Zuckerman DM, Arantes GM. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. Biophys J 2019. [PMID: 29539393 DOI: 10.1016/j.bpj.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
21
Burley KH, Gill SC, Lim NM, Mobley DL. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo. J Chem Theory Comput 2019;15:1848-1862. [PMID: 30677291 DOI: 10.1021/acs.jctc.8b01018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
22
Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. Biophys J 2019;116:205-214. [PMID: 30606449 PMCID: PMC6349996 DOI: 10.1016/j.bpj.2018.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 06/23/2018] [Accepted: 09/27/2018] [Indexed: 12/23/2022]  Open
23
Brotzakis ZF, Parrinello M. Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables. J Chem Theory Comput 2018;15:1393-1398. [DOI: 10.1021/acs.jctc.8b00827] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
24
Wang Y, Martins JM, Lindorff-Larsen K. Biomolecular conformational changes and ligand binding: from kinetics to thermodynamics. Chem Sci 2017;8:6466-6473. [PMID: 29619200 PMCID: PMC5859887 DOI: 10.1039/c7sc01627a] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022]  Open
25
Miao Y, McCammon JA. Gaussian Accelerated Molecular Dynamics: Theory, Implementation, and Applications. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2017;13:231-278. [PMID: 29720925 PMCID: PMC5927394 DOI: 10.1016/bs.arcc.2017.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
26
Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE. Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. Biophys J 2017;111:1631-1640. [PMID: 27760351 DOI: 10.1016/j.bpj.2016.08.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 01/07/2023]  Open
27
Xie B, Nguyen TH, Minh DDL. Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations. J Chem Theory Comput 2017;13:2930-2944. [PMID: 28430432 PMCID: PMC5612505 DOI: 10.1021/acs.jctc.6b01183] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
28
Mobley DL, Gilson MK. Predicting Binding Free Energies: Frontiers and Benchmarks. Annu Rev Biophys 2017;46:531-558. [PMID: 28399632 PMCID: PMC5544526 DOI: 10.1146/annurev-biophys-070816-033654] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
29
Budiardjo SJ, Licknack TJ, Cory MB, Kapros D, Roy A, Lovell S, Douglas J, Karanicolas J. Full and Partial Agonism of a Designed Enzyme Switch. ACS Synth Biol 2016;5:1475-1484. [PMID: 27389009 DOI: 10.1021/acssynbio.6b00097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
30
Consentius P, Gohlke U, Loll B, Alings C, Müller R, Heinemann U, Kaupp M, Wahl M, Risse T. Tracking Transient Conformational States of T4 Lysozyme at Room Temperature Combining X-ray Crystallography and Site-Directed Spin Labeling. J Am Chem Soc 2016;138:12868-12875. [DOI: 10.1021/jacs.6b05507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
31
Lee H, Fischer M, Shoichet BK, Liu SY. Hydrogen Bonding of 1,2-Azaborines in the Binding Cavity of T4 Lysozyme Mutants: Structures and Thermodynamics. J Am Chem Soc 2016;138:12021-4. [PMID: 27603116 DOI: 10.1021/jacs.6b06566] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
32
Wang Y, Papaleo E, Lindorff-Larsen K. Mapping transiently formed and sparsely populated conformations on a complex energy landscape. eLife 2016;5. [PMID: 27552057 PMCID: PMC5050026 DOI: 10.7554/elife.17505] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022]  Open
33
Lim NM, Wang L, Abel R, Mobley DL. Sensitivity in Binding Free Energies Due to Protein Reorganization. J Chem Theory Comput 2016;12:4620-31. [PMID: 27462935 DOI: 10.1021/acs.jctc.6b00532] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
34
Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016;116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
35
Miao Y, Feher VA, McCammon JA. Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation. J Chem Theory Comput 2015;11:3584-3595. [PMID: 26300708 PMCID: PMC4535365 DOI: 10.1021/acs.jctc.5b00436] [Citation(s) in RCA: 474] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 12/20/2022]
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