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For: Ornstein RL. Using molecular dynamics simulations on crambin to evaluate the suitability of different continuum dielectric and hydrogen atom models for protein simulations. J Biomol Struct Dyn 1990;7:1019-41. [PMID: 2360995 DOI: 10.1080/07391102.1990.10508543] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Number Cited by Other Article(s)
1
Abaturov LV, Nosova NG. Structure of crambin in solution, crystal and in the trajectories of molecular dynamics simulations. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913030020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
2
Takahashi T, Sugiura J, Nagayama K. Comparison of all atom, continuum, and linear fitting empirical models for charge screening effect of aqueous medium surrounding a protein molecule. J Chem Phys 2002. [DOI: 10.1063/1.1468222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
3
Caves LS, Evanseck JD, Karplus M. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin. Protein Sci 1998;7:649-66. [PMID: 9541397 PMCID: PMC2143962 DOI: 10.1002/pro.5560070314] [Citation(s) in RCA: 372] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
4
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]
5
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]
6
Grubmüller H, Tavan P. Molecular dynamics of conformational substates for a simplified protein model. J Chem Phys 1994. [DOI: 10.1063/1.467427] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
7
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] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
8
Bass MB, Ornstein RL. Substrate specificity of cytochrome P450cam forL- andD- norcamphor as studied by molecular dynamics simulations. J Comput Chem 1993. [DOI: 10.1002/jcc.540140506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
9
Ahlers M, Grainger DW, Herron JN, Lim K, Ringsdorf H, Salesse C. Quenching of fluorescein-conjugated lipids by antibodies. Quantitative recognition and binding of lipid-bound haptens in biomembrane models, formation of two-dimensional protein domains and molecular dynamics simulations. Biophys J 1992;63:823-38. [PMID: 1420916 PMCID: PMC1262215 DOI: 10.1016/s0006-3495(92)81645-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
10
Guenot J, Kollman PA. Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor. Protein Sci 1992;1:1185-205. [PMID: 1304396 PMCID: PMC2142173 DOI: 10.1002/pro.5560010912] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
11
Bass MB, Paulsen MD, Ornstein RL. Substrate mobility in a deeply buried active site: analysis of norcamphor bound to cytochrome P-450cam as determined by a 201-psec molecular dynamics simulation. Proteins 1992;13:26-37. [PMID: 1594575 DOI: 10.1002/prot.340130103] [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: 12/27/2022]
12
Bass MB, Hopkins DF, Jaquysh WA, Ornstein RL. A method for determining the positions of polar hydrogens added to a protein structure that maximizes protein hydrogen bonding. Proteins 1992;12:266-77. [PMID: 1372979 DOI: 10.1002/prot.340120305] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
13
Paulsen MD, Ornstein RL. A 175-psec molecular dynamics simulation of camphor-bound cytochrome P-450cam. Proteins 1991;11:184-204. [PMID: 1749772 DOI: 10.1002/prot.340110304] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
14
Paulsen MD, Bass MB, Ornstein RL. Analysis of active site motions from a 175 picosecond molecular dynamics simulation of camphor-bound cytochrome P450cam. J Biomol Struct Dyn 1991;9:187-203. [PMID: 1741957 DOI: 10.1080/07391102.1991.10507906] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
15
Cornell WD, Howard AE, Kollman P. Molecular mechanical potential functions and their application to study molecular systems. Curr Opin Struct Biol 1991. [DOI: 10.1016/0959-440x(91)90062-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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