Molecular modeling

Current Opinion in Chemical Biology

Volumn 1, Issue 3, 1997, Pages 392-398

  Broughton, Howard B ^a  

^a NEUROSCIENCE RESEARCH CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER; SOLVENT;

CHEMICAL STRUCTURE; CHEMISTRY; DATA BASE; REVIEW; STRUCTURE ACTIVITY RELATION;

BIOPOLYMERS; DATABASE MANAGEMENT SYSTEMS; MODELS, MOLECULAR; SOLVENTS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0031244216     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(97)80079-8     Document Type: Article

References (76)

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31. Rao BG, Kim EE, Murcko MA: Calculation of solvation and binding free energy differences between VX-478 and its analogs by free energy perturbation and AMSOL methods. J Comput-Aided Mol Des 1996, 10:23-30. A comparison of two completely different methods of accounting for solvation effects in a practical application.
32. Kroemer RT, Hecht P, Liedl KR: Different electrostatic descriptors in comparative molecular field analysis: a comparison of molecular electrostatic and Coulomb potentials. J Comput Chem 1996, 17:1296-1308. Compares several ways of obtaining the electrostatic descriptors for this popular quantitative structure-activity relationship (QSAR) method and identifies the most suitable.
33. Dunn WJ, Hopfinger AJ, Catana C, Duraiswami C: Solution of the conformation and alignment tensors for the binding of trimethoprim and its analogs to dihydrofolate reductase: 3D-quantitative structure-activity relationship study using molecular shape analysis, 3-way partial least-squares regression, and 3-way factor analysis. J Med Chem 1996, 39:4825-4832. Describes a method capable of simultaneously considering conformation, orientation, nature and activity of molecules in a quantitative structure-activity relationship analysis.
34. Thorner DA, Willett P, Wright PM, Taylor R: Similarity searching in files of three-dimensional chemical structures: representation and searching of molecular electrostatic potentials using field-graphs. J Comput-Aided Mol Des 1997, 11:163-174. Describes a database system able to identify structures whose molecular electrostatic potentials are similar to that of a probe structure.
35. Thorner DA, Wild DJ, Willett P, Wright PM: Similarity searching in files of three-dimensional chemical structures: flexible field-based searching of molecular electrostatic potentials. J Chem Inform Comput Sci 1996, 36:900-908. Amplifies on the work of Thorner et al. (1997) [34•] by permitting the molecules to be flexible - a molecule will be found if by changing conformation it can have a molecular electrostatic potential similar to the probe molecule.
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47. Sponer J, Leszczynski J, Hobza P: Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations. J Comput Chem 1996, 17:841-850. Discusses how well newer and computationally cheaper approaches model the interaction between stacked cytosines, compared to high quality ab initio calculations.
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71. Perlman JH, Laakkonen, LJ, Guarnieri F, Osman R, Gershengorn MC: A refined model of the thyrotropin-releasing hormone (TRH) receptor binding pocket. Experimental analysis and energy minimization of the complex between TRH and TRH receptor. Biochemistry 1996, 35:7643-7650.
72. Laakkonen LJ, Guarnieri F, Perlman JH, Gershengorn MC, Osman R: A refined model of the thyrotropin-releasing hormone (TRH) receptor binding pocket. Novel mixed-mode Monte Carlo/stochastic dynamics simulations of the complex between TRH and TRH receptor. Biochemistry 1996, 35:7651-7663.
73. Todorov NP, Dean PM: Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. J Comput-Aided Mol Des 1997, 2:175-192.
74. Gschwend DA, Kuntz ID: Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. J Comput-Aided Mol Des 1996, 10:123-132.
75. Rarey M, Kramer B, Lengauer T, Klebe G: A fast flexible docking method using and incremental construction algorithm. J Mol Biol 1996, 261:470-489.
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