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For: Arnold GE, Ornstein RL. An evaluation of implicit and explicit solvent model systems for the molecular dynamics simulation of bacteriophage T4 lysozyme. Proteins 1994;18:19-33. [PMID: 8146120 DOI: 10.1002/prot.340180105] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Number Cited by Other Article(s)
1
Machine learning/molecular dynamic protein structure prediction approach to investigate the protein conformational ensemble. Sci Rep 2022;12:10018. [PMID: 35705565 PMCID: PMC9200820 DOI: 10.1038/s41598-022-13714-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 05/11/2022] [Indexed: 11/25/2022]  Open
2
Chakravorty A, Jia Z, Li L, Zhao S, Alexov E. Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling. J Chem Theory Comput 2018;14:1020-1032. [PMID: 29350933 PMCID: PMC9885857 DOI: 10.1021/acs.jctc.7b00756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
3
Silveira AJ, Abreu CRA. Molecular dynamics with rigid bodies: Alternative formulation and assessment of its limitations when employed to simulate liquid water. J Chem Phys 2017;147:124104. [DOI: 10.1063/1.5003636] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
4
Chang KJ, Kuo YH, Chiang YW. Study of Protein Dynamics under Nanoconfinement by Spin-Label ESR: A Case of T4 Lysozyme Protein. J Phys Chem B 2017;121:4355-4363. [DOI: 10.1021/acs.jpcb.7b00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
5
Lingenheil M, Denschlag R, Reichold R, Tavan P. The "Hot-Solvent/Cold-Solute" Problem Revisited. J Chem Theory Comput 2015;4:1293-306. [PMID: 26631705 DOI: 10.1021/ct8000365] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
6
Zheng W, Glenn P. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation. J Chem Phys 2015;142:035101. [PMID: 25612731 DOI: 10.1063/1.4905606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
7
Direct observation of T4 lysozyme hinge-bending motion by fluorescence correlation spectroscopy. Biophys J 2012;103:1525-36. [PMID: 23062345 DOI: 10.1016/j.bpj.2012.07.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 10/27/2022]  Open
8
Meirovitch E. SRLS analysis of 15N relaxation from bacteriophage T4 lysozyme: a tensorial perspective that features domain motion. J Phys Chem B 2012;116:6118-27. [PMID: 22568692 DOI: 10.1021/jp301999n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
9
Fenn TD, Schnieders MJ, Brunger AT. A smooth and differentiable bulk-solvent model for macromolecular diffraction. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010;66:1024-31. [PMID: 20823553 PMCID: PMC2935282 DOI: 10.1107/s0907444910031045] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 08/03/2010] [Indexed: 12/05/2022]
10
Eastwood MP, Stafford KA, Lippert RA, Jensen MØ, Maragakis P, Predescu C, Dror RO, Shaw DE. Equipartition and the Calculation of Temperature in Biomolecular Simulations. J Chem Theory Comput 2010;6:2045-58. [DOI: 10.1021/ct9002916] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
11
Fajer MI, Li H, Yang W, Fajer PG. Mapping electron paramagnetic resonance spin label conformations by the simulated scaling method. J Am Chem Soc 2007;129:13840-6. [PMID: 17948993 DOI: 10.1021/ja071404v] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
12
Kowadlo G, Hall NE, Burgess AW. De novo design of beta-helical polypeptides. Growth Factors 2007;25:168-90. [PMID: 18049953 DOI: 10.1080/08977190701679772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
13
A severe artifact in simulation of liquid water using a long cut-off length: Appearance of a strange layer structure. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2005.02.073] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
14
Stoica I. Solvent Interactions and Protein Dynamics in Spin-labeled T4 Lysozyme. J Biomol Struct Dyn 2004;21:745-60. [PMID: 15106997 DOI: 10.1080/07391102.2004.10506965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
15
Król M. Comparison of various implicit solvent models in molecular dynamics simulations of immunoglobulin G light chain dimer. J Comput Chem 2003;24:531-46. [PMID: 12632469 DOI: 10.1002/jcc.10186] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
16
Hassan SA, Mehler EL, Zhang D, Weinstein H. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials. Proteins 2003;51:109-25. [PMID: 12596268 DOI: 10.1002/prot.10330] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
17
Bystroff C. MASKER: improved solvent-excluded molecular surface area estimations using Boolean masks. Protein Eng Des Sel 2002;15:959-65. [PMID: 12601135 DOI: 10.1093/protein/15.12.959] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
18
Chakrabarti S, Dasgupta D, Bhattacharyya D. Role of mg2+ in chromomycin a3 - DNA interaction: a molecular modeling study. J Biol Phys 2000;26:203-18. [PMID: 23345722 PMCID: PMC3456754 DOI: 10.1023/a:1010397526355] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
19
Bandyopadhyay D, Bhattacharyya D. Effect of neighboring bases on base-pair stacking orientation: a molecular dynamics study. J Biomol Struct Dyn 2000;18:29-43. [PMID: 11021650 DOI: 10.1080/07391102.2000.10506645] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
20
Garemyr R, Elofsson A. Study of the electrostatics treatment in molecular dynamics simulations. Proteins 1999;37:417-28. [PMID: 10591101 DOI: 10.1002/(sici)1097-0134(19991115)37:3<417::aid-prot9>3.0.co;2-u] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
21
Arnold GE, Ornstein RL. Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3. Biophys J 1997;73:1147-59. [PMID: 9284282 PMCID: PMC1181014 DOI: 10.1016/s0006-3495(97)78147-5] [Citation(s) in RCA: 78] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
22
Komeiji Y, Uebayasi M, Takata R, Shimizu A, Itsukashi K, Taiji M. Fast and accurate molecular dynamics simulation of a protein using a special-purpose computer. J Comput Chem 1997. [DOI: 10.1002/(sici)1096-987x(199709)18:12<1546::aid-jcc11>3.0.co;2-i] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
23
Lozano JJ, López-de-Briñas E, Centeno NB, Guigó R, Sanz F. Three-dimensional modelling of human cytochrome P450 1A2 and its interaction with caffeine and MeIQ. J Comput Aided Mol Des 1997;11:395-408. [PMID: 9334905 DOI: 10.1023/a:1007947411145] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
24
Arnold GE, Ornstein RL. Protein hinge bending as seen in molecular dynamics simulations of native and M61 mutant T4 lysozymes. Biopolymers 1997;41:533-44. [PMID: 9095676 DOI: 10.1002/(sici)1097-0282(19970415)41:5<533::aid-bip5>3.0.co;2-n] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
25
Kandadai NS, Reddy MR. Solution structure of papain as studied by molecular mechanics and molecular dynamics techniques. J Comput Chem 1996;17:1328-38. [DOI: 10.1002/(sici)1096-987x(199608)17:11<1328::aid-jcc5>3.0.co;2-o] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/1995] [Accepted: 11/19/1995] [Indexed: 11/09/2022]
26
Manchester JI, Paulsen MD, Rein R, Ornstein RL. 1,1,1-Trichloroethane-bound cytochrome P450cam dynamics. Does active site water make a difference? Chem Phys 1996. [DOI: 10.1016/0301-0104(95)00412-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
27
Blackledge MJ, Guerlesquin F, Marion D. Comparison of low oxidoreduction potential cytochrome c553 from Desulfovibrio vulgaris with the class I cytochrome c family. Proteins 1996;24:178-94. [PMID: 8820485 DOI: 10.1002/(sici)1097-0134(199602)24:2<178::aid-prot5>3.0.co;2-f] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
28
Manchester JI, Ornstein RL. Rational approach to improving reductive catalysis by cytochrome P450cam. Biochimie 1996;78:714-22. [PMID: 9010600 DOI: 10.1016/s0300-9084(97)82529-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
29
Manchester JI, Ornstein RL. Molecular dynamics simulations indicate that F87W,T185F-cytochrome P450cam may reductively dehalogenate 1,1,1-trichloroethane. J Biomol Struct Dyn 1995;13:413-22. [PMID: 8825721 DOI: 10.1080/07391102.1995.10508851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
30
Troyer JM, Cohen FE. Protein conformational landscapes: energy minimization and clustering of a long molecular dynamics trajectory. Proteins 1995;23:97-110. [PMID: 8539254 DOI: 10.1002/prot.340230111] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
31
Sankararamakrishnan R, Sansom MS. Structural features of isolated M2 helices of nicotinic receptors. Simulated annealing via molecular dynamics studies. Biophys Chem 1995;55:215-30. [PMID: 7626742 DOI: 10.1016/0301-4622(95)00006-j] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
32
Evans JS, Mathiowetz AM, Chan SI, Goddard WA. De novo prediction of polypeptide conformations using dihedral probability grid Monte Carlo methodology. Protein Sci 1995;4:1203-16. [PMID: 7549884 PMCID: PMC2143148 DOI: 10.1002/pro.5560040618] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
33
Benoit JP, Doucet J. Diffuse scattering in protein crystallography. Q Rev Biophys 1995;28:131-69. [PMID: 7568674 DOI: 10.1017/s0033583500003048] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
34
Bravi G, Legname G, Chan AW. Substrate recognition by ribosome-inactivating protein studied by molecular modeling and molecular electrostatic potentials. JOURNAL OF MOLECULAR GRAPHICS 1995;13:83-8, 109. [PMID: 7619790 DOI: 10.1016/0263-7855(94)00014-j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
35
Paulsen MD, Ornstein RL. Dramatic differences in the motions of the mouth of open and closed cytochrome P450BM-3 by molecular dynamics simulations. Proteins 1995;21:237-43. [PMID: 7784427 DOI: 10.1002/prot.340210306] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
36
Braatz JA, Bass MB, Ornstein RL. An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2. J Comput Aided Mol Des 1994;8:607-22. [PMID: 7876903 DOI: 10.1007/bf00123668] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
37
Arnold GE, Manchester JI, Townsend BD, Ornstein RL. Investigation of domain motions in bacteriophage T4 lysozyme. J Biomol Struct Dyn 1994;12:457-74. [PMID: 7702780 DOI: 10.1080/07391102.1994.10508751] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
38
Paulsen MD, Ornstein RL. Active-site mobility inhibits reductive dehalogenation of 1,1,1-trichloroethane by cytochrome P450cam. J Comput Aided Mol Des 1994;8:389-404. [PMID: 7815091 DOI: 10.1007/bf00125374] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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