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For: Liu Z, Ensing B, Moore PB. Quantitative Assessment of Force Fields on Both Low-Energy Conformational Basins and Transition-State Regions of the (ϕ-ψ) Space. J Chem Theory Comput 2010;7:402-19. [PMID: 26596162 DOI: 10.1021/ct100395n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Number Cited by Other Article(s)
1
Lewis-Atwell T, Townsend PA, Grayson MN. Comparisons of different force fields in conformational analysis and searching of organic molecules: A review. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131865] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
2
Correct folding of an α-helix and a β-hairpin using a polarized 2D torsional potential. Sci Rep 2015;5:10359. [PMID: 26039188 PMCID: PMC5380191 DOI: 10.1038/srep10359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/09/2015] [Indexed: 01/12/2023]  Open
3
Tzanov AT, Cuendet MA, Tuckerman ME. How Accurately Do Current Force Fields Predict Experimental Peptide Conformations? An Adiabatic Free Energy Dynamics Study. J Phys Chem B 2014;118:6539-52. [DOI: 10.1021/jp500193w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
4
Reppert M, Tokmakoff A. Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment. J Chem Phys 2013;138:134116. [PMID: 23574217 DOI: 10.1063/1.4798938] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
5
Li Y, Gao Y, Zhang X, Wang X, Mou L, Duan L, He X, Mei Y, Zhang JZH. A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation. J Mol Model 2013;19:3647-57. [PMID: 23765039 DOI: 10.1007/s00894-013-1879-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 05/01/2013] [Indexed: 11/29/2022]
6
Elder R, Jayaraman A. Sequence-specific recognition of cancer drug-DNA adducts by HMGB1a repair protein. Biophys J 2012;102:2331-8. [PMID: 22677386 PMCID: PMC3353062 DOI: 10.1016/j.bpj.2012.04.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/05/2012] [Accepted: 04/09/2012] [Indexed: 01/16/2023]  Open
7
Cruz VL, Ramos J, Martinez-Salazar J. Assessment of the intrinsic conformational preferences of dipeptide amino acids in aqueous solution by combined umbrella sampling/MBAR statistics. A comparison with experimental results. J Phys Chem B 2011;116:469-75. [PMID: 22136632 DOI: 10.1021/jp206757j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
8
Jaillet L, Corcho FJ, Pérez JJ, Cortés J. Randomized tree construction algorithm to explore energy landscapes. J Comput Chem 2011;32:3464-74. [DOI: 10.1002/jcc.21931] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 07/05/2011] [Accepted: 08/02/2011] [Indexed: 11/09/2022]
9
Grouleff J, Jensen F. Searching Peptide Conformational Space. J Chem Theory Comput 2011;7:1783-90. [DOI: 10.1021/ct200161e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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