MolSurfer: A macromolecular interface navigator

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3349-3351

  Gabdoulline, Razif R ^a   Wade, Rebecca C ^a,b   Walther, Dirk ^c  

^a European Media Laboratory   (Germany)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c Department of Life Sciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; LIGAND; PROTEIN;

ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DNA PROTEIN COMPLEX; ELECTRIC POTENTIAL; EXPERIMENTAL DESIGN; HYDROPHOBICITY; MACROMOLECULE; NUCLEIC ACID ANALYSIS; ONLINE SYSTEM; PEPTIDE MAPPING; PHYSICAL CHEMISTRY; POISSON DISTRIBUTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRICITY; INTERNET; METABOLISM;

COMPUTER GRAPHICS; DATABASES, PROTEIN; DNA; ELECTROSTATICS; HYDROPHOBICITY; INTERNET; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEINS; RNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0042622392     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg588     Document Type: Article

References (12)

1. Gabdoulline,R.R., Wade,R.C. and Walther,D. (1999) MolSurfer: two dimensional maps for navigating three-dimensional structures of proteins. Trends Biochem. Sci., 24, 285-287.
2. Luedemann,S.K., Gabdoulline,R.R., Lounnas,V. and Wade,R.C. (2001) Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: an interactive look at the underlying mechanisms. Internet. J. Chem., 4, 6 (www.ijc.com/articles/2001v4/6/).
3. Gabdoulline,R.R. and Wade,R.C. (1996) Analitically defined surfaces to analyze molecular interaction properties. J. Mol. Graph., 14, 341-353.
4. Walther,D. (1997) WebMol - a Java based PDB viewer. Trends Biochem. Sci., 22, 274-275.
5. Eisenberg,D., Wesson,M. and Yamashita,M. (1989) Interpretation of protein folding and binding with atomic solvation parameters. Chem. Scripta, 29A, 217-221.
6. Shih,P., Pedersen,L.G., Gibbs,P.R. and Wolfensen,R. (1998) Hydrophobicities of the nucleic acid bases: distribution coefficients from water to cyclohexane. J. Mol. Biol., 280, 421-430.
7. Madura,J.D., Briggs,J.M., Wade,R.C., Davis,M.E., Luty,B.A., Ilin,A., Antosiewicz,J., Gilson,M.K., Bagheri,B., Scott,L.R. and McCammon,J.A. (1995) Electrostatic and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comp. Phys. Comm., 91, 57-95.
8. Bogan,A.A. and Thorn,K.S. (1998) Anatomy of hot spots in protein interfaces. J. Mol. Biol., 280, 1-9.
9. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
10. McCoy,A.J., Chandana,E.V. and Colman,P.M. (1997) Electrostatic complementarity at protein/protein interfaces. J. Mol. Biol., 268, 570-584.
11. Nielsen,J.E., Andersen,K.V., Honig,B., Hooft,R.W., Klebe,G., Vriend,G. and Wade,R.C. (1999) Improving macromolecular electrostatics calculations. Protein Eng., 12, 657-662.
12. Nadassy,K., Wodak,S.J. and Janin,J. (1999) Structural features of protein-nucleic acid recognition sites. Biochemistry, 38, 1999-2017.