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For: Carstensen T, Farrell D, Huang Y, Baker NA, Nielsen JE. On the development of protein pKa calculation algorithms. Proteins 2011;79:3287-98. [PMID: 21744393 DOI: 10.1002/prot.23091] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/16/2011] [Accepted: 05/04/2011] [Indexed: 11/10/2022]
Number Cited by Other Article(s)
1
Fossat MJ, Pappu RV. q-Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides. J Phys Chem B 2019;123:6952-6967. [PMID: 31362509 PMCID: PMC10785832 DOI: 10.1021/acs.jpcb.9b05206] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
2
Barroso da Silva FL, Sterpone F, Derreumaux P. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. J Chem Theory Comput 2019;15:3875-3888. [DOI: 10.1021/acs.jctc.9b00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
3
Liu J, Swails J, Zhang JZH, He X, Roitberg AE. A Coupled Ionization-Conformational Equilibrium Is Required To Understand the Properties of Ionizable Residues in the Hydrophobic Interior of Staphylococcal Nuclease. J Am Chem Soc 2018;140:1639-1648. [PMID: 29308643 DOI: 10.1021/jacs.7b08569] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
4
Barroso daSilva FL, Dias LG. Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems. Biophys Rev 2017;9:699-728. [PMID: 28921104 PMCID: PMC5662048 DOI: 10.1007/s12551-017-0311-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/01/2017] [Indexed: 12/20/2022]  Open
5
Barroso da Silva FL, Derreumaux P, Pasquali S. Fast coarse-grained model for RNA titration. J Chem Phys 2017;146:035101. [PMID: 28109220 DOI: 10.1063/1.4972986] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
6
Barroso da Silva FL, MacKernan D. Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations. J Chem Theory Comput 2017;13:2915-2929. [DOI: 10.1021/acs.jctc.6b01114] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
7
Li L, Chakravorty A, Alexov E. DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem 2017;38:584-593. [PMID: 28130775 PMCID: PMC5315605 DOI: 10.1002/jcc.24715] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/10/2016] [Indexed: 12/31/2022]
8
Wu X, Lee J, Brooks BR. Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water. J Phys Chem B 2016;121:3318-3330. [PMID: 27700118 DOI: 10.1021/acs.jpcb.6b08249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
9
Lee J, Miller BT, Damjanović A, Brooks BR. Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method. J Chem Theory Comput 2015;11:2560-74. [PMID: 26575555 DOI: 10.1021/ct501101f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
10
Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/471836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
11
Kukic P, Farrell D, McIntosh LP, García-Moreno E B, Jensen KS, Toleikis Z, Teilum K, Nielsen JE. Protein dielectric constants determined from NMR chemical shift perturbations. J Am Chem Soc 2013;135:16968-76. [PMID: 24124752 DOI: 10.1021/ja406995j] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Gosink LJ, Hogan EA, Pulsipher TC, Baker NA. Bayesian model aggregation for ensemble-based estimates of protein pKa values. Proteins 2013;82:354-63. [PMID: 23946048 DOI: 10.1002/prot.24390] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/10/2013] [Accepted: 07/26/2013] [Indexed: 12/14/2022]
13
Kilambi KP, Gray JJ. Rapid calculation of protein pKa values using Rosetta. Biophys J 2013;103:587-595. [PMID: 22947875 DOI: 10.1016/j.bpj.2012.06.044] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 06/08/2012] [Accepted: 06/11/2012] [Indexed: 12/21/2022]  Open
14
Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012;45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
15
Johnston MA, Farrell D, Nielsen JE. A collaborative environment for developing and validating predictive tools for protein biophysical characteristics. J Comput Aided Mol Des 2012;26:387-96. [DOI: 10.1007/s10822-012-9564-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/18/2012] [Indexed: 11/29/2022]
16
Nielsen JE, Gunner MR, Bertrand García-Moreno E. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 2011;79:3249-59. [PMID: 22002877 PMCID: PMC3375608 DOI: 10.1002/prot.23194] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 09/13/2011] [Indexed: 12/13/2022]
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