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For: Wallace JA, Shen JK. Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. J Chem Phys 2013;137:184105. [PMID: 23163362 DOI: 10.1063/1.4766352] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
Number Cited by Other Article(s)
51
Socher E, Sticht H. Probing the Structure of the Escherichia coli Periplasmic Proteins HdeA and YmgD by Molecular Dynamics Simulations. J Phys Chem B 2016;120:11845-11855. [PMID: 27787971 DOI: 10.1021/acs.jpcb.6b06091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
52
Giard A, Filhol JS, Jolibois F, Cavelier F, Berthomieu D. Prediction of pKa Using DFT: the Nicotianamine Polyacid Example. J Chem Theory Comput 2016;12:5493-5500. [DOI: 10.1021/acs.jctc.6b00404] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
53
Huang Y, Chen W, Wallace JA, Shen J. All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water. J Chem Theory Comput 2016;12:5411-5421. [PMID: 27709966 DOI: 10.1021/acs.jctc.6b00552] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
54
Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi X, Shen J, Kelly DL, Ghodssi R, Bentley WE, Payne GF. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels. Adv Healthc Mater 2016;5:2595-2616. [PMID: 27616350 PMCID: PMC5485850 DOI: 10.1002/adhm.201600516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/26/2016] [Indexed: 12/14/2022]
55
Schimka S, Santer S, Mujkić-Ninnemann NM, Bléger D, Hartmann L, Wehle M, Lipowsky R, Santer M. Photosensitive Peptidomimetic for Light-Controlled, Reversible DNA Compaction. Biomacromolecules 2016;17:1959-68. [DOI: 10.1021/acs.biomac.6b00052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
56
Ellis CR, Tsai CC, Hou X, Shen J. Constant pH Molecular Dynamics Reveals pH-Modulated Binding of Two Small-Molecule BACE1 Inhibitors. J Phys Chem Lett 2016;7:944-9. [PMID: 26905811 PMCID: PMC5713896 DOI: 10.1021/acs.jpclett.6b00137] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
57
Donnini S, Ullmann RT, Groenhof G, Grubmüller H. Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer. J Chem Theory Comput 2016;12:1040-51. [PMID: 26881315 DOI: 10.1021/acs.jctc.5b01160] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
58
Davis CM, Dyer RB. The Role of Electrostatic Interactions in Folding of β-Proteins. J Am Chem Soc 2016;138:1456-64. [PMID: 26750867 DOI: 10.1021/jacs.5b13201] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
59
Morrow BH, Eike DM, Murch BP, Koenig PH, Shen JK. Predicting proton titration in cationic micelle and bilayer environments. J Chem Phys 2015;141:084714. [PMID: 25173037 DOI: 10.1063/1.4893439] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
60
Morrow BH, Payne GF, Shen J. pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape. J Am Chem Soc 2015;137:13024-30. [PMID: 26383701 DOI: 10.1021/jacs.5b07761] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
61
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]
62
Vila-Viçosa D, Teixeira VH, Baptista AM, Machuqueiro M. Constant-pH MD Simulations of an Oleic Acid Bilayer. J Chem Theory Comput 2015;11:2367-76. [DOI: 10.1021/acs.jctc.5b00095] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
63
Protein flexibility and cysteine reactivity: influence of mobility on the H-bond network and effects on pKa prediction. Protein J 2015;33:323-36. [PMID: 24809821 DOI: 10.1007/s10930-014-9564-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
64
Dissanayake T, Swails JM, Harris ME, Roitberg AE, York DM. Interpretation of pH-activity profiles for acid-base catalysis from molecular simulations. Biochemistry 2015;54:1307-13. [PMID: 25615525 DOI: 10.1021/bi5012833] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
65
Reif MM, Oostenbrink C. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization. Theor Chem Acc 2015;134:2. [PMID: 26097404 PMCID: PMC4470580 DOI: 10.1007/s00214-014-1600-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
66
Vila-Viçosa D, Teixeira VH, Santos HAF, Baptista AM, Machuqueiro M. Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers. J Chem Theory Comput 2014;10:5483-92. [DOI: 10.1021/ct500680q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
67
Chen W, Shen JK. Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics. J Comput Chem 2014;35:1986-96. [PMID: 25142416 PMCID: PMC4165709 DOI: 10.1002/jcc.23713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/20/2014] [Accepted: 08/03/2014] [Indexed: 12/21/2022]
68
Cote Y, Fu IW, Dobson ET, Goldberger JE, Nguyen HD, Shen JK. Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2014;118:16272-16278. [PMID: 25089166 PMCID: PMC4111372 DOI: 10.1021/jp5048024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/27/2014] [Indexed: 05/23/2023]
69
Lee J, Miller BT, Damjanović A, Brooks BR. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. J Chem Theory Comput 2014;10:2738-2750. [PMID: 25061443 PMCID: PMC4095908 DOI: 10.1021/ct500175m] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 12/21/2022]
70
Chen W, Morrow BH, Shi C, Shen JK. Recent development and application of constant pH molecular dynamics. MOLECULAR SIMULATION 2014;40:830-838. [PMID: 25309035 DOI: 10.1080/08927022.2014.907492] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
71
Chen W, Wallace JA, Yue Z, Shen JK. Introducing titratable water to all-atom molecular dynamics at constant pH. Biophys J 2014;105:L15-7. [PMID: 23972860 DOI: 10.1016/j.bpj.2013.06.036] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2013] [Revised: 06/06/2013] [Accepted: 06/25/2013] [Indexed: 11/25/2022]  Open
72
Swails JM, York DM, Roitberg AE. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation. J Chem Theory Comput 2014;10:1341-1352. [PMID: 24803862 PMCID: PMC3985686 DOI: 10.1021/ct401042b] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Indexed: 12/24/2022]
73
Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins 2014;82:1319-31. [PMID: 24375620 DOI: 10.1002/prot.24499] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 11/13/2013] [Accepted: 12/12/2013] [Indexed: 12/14/2022]
74
Morrow BH, Koenig PH, Shen JK. Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013;29:14823-14830. [PMID: 24215478 PMCID: PMC3946477 DOI: 10.1021/la403398n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
75
Morrow BH, Koenig PH, Shen JK. Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids. J Chem Phys 2013. [PMID: 23181330 DOI: 10.1063/1.4766313] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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