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For: Hocky GM, Dannenhoffer-Lafage T, Voth GA. Coarse-Grained Directed Simulation. J Chem Theory Comput 2017;13:4593-4603. [PMID: 28800392 DOI: 10.1021/acs.jctc.7b00690] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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
Gilardoni I, Piomponi V, Fröhlking T, Bussi G. MDRefine: A Python package for refining molecular dynamics trajectories with experimental data. J Chem Phys 2025;162:192501. [PMID: 40371829 DOI: 10.1063/5.0256841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Accepted: 04/28/2025] [Indexed: 05/16/2025]  Open
2
Sasmal S, Pal T, Hocky GM, McCullagh M. Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM. J Chem Theory Comput 2024;20:3492-3502. [PMID: 38662196 PMCID: PMC11104435 DOI: 10.1021/acs.jctc.4c00223] [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: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
3
Gomez D, Peña Ccoa WJ, Singh Y, Rojas E, Hocky GM. Molecular Paradigms for Biological Mechanosensing. J Phys Chem B 2021;125:12115-12124. [PMID: 34709040 DOI: 10.1021/acs.jpcb.1c06330] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
4
Cui Q, Pal T, Xie L. Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"? J Phys Chem B 2021;125:689-702. [PMID: 33401903 PMCID: PMC8360698 DOI: 10.1021/acs.jpcb.0c09898] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
5
Amirkulova DB, Chakraborty M, White AD. Experimentally Consistent Simulation of Aβ21-30 Peptides with a Minimal NMR Bias. J Phys Chem B 2020;124:8266-8277. [PMID: 32845146 DOI: 10.1021/acs.jpcb.0c07129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
6
Calio PB, Hocky GM, Voth GA. Minimal Experimental Bias on the Hydrogen Bond Greatly Improves Ab Initio Molecular Dynamics Simulations of Water. J Chem Theory Comput 2020;16:5675-5684. [DOI: 10.1021/acs.jctc.0c00558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
7
Hartmann MJ, Singh Y, Vanden-Eijnden E, Hocky GM. Infinite switch simulated tempering in force (FISST). J Chem Phys 2020;152:244120. [DOI: 10.1063/5.0009280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
8
Amirkulova DB, White AD. Recent advances in maximum entropy biasing techniques for molecular dynamics. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1608988] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
9
Bussi G, Tribello GA. Analyzing and Biasing Simulations with PLUMED. Methods Mol Biol 2019;2022:529-578. [PMID: 31396917 DOI: 10.1007/978-1-4939-9608-7_21] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
10
Advances in coarse-grained modeling of macromolecular complexes. Curr Opin Struct Biol 2018;52:119-126. [PMID: 30508766 DOI: 10.1016/j.sbi.2018.11.005] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/05/2018] [Accepted: 11/17/2018] [Indexed: 01/12/2023]
11
Capelli R, Tiana G, Camilloni C. An implementation of the maximum-caliber principle by replica-averaged time-resolved restrained simulations. J Chem Phys 2018;148:184114. [PMID: 29764124 DOI: 10.1063/1.5030339] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
12
Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments. COMPUTATION 2018. [DOI: 10.3390/computation6010015] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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