Evaluation of the protein solvent-accessible surface using reduced representations in terms of critical points of the electron density

Journal of Computational Chemistry

Volumn 25, Issue 9, 2004, Pages 1117-1126

  Becue, A ^a   Meurice, N ^a   Leherte, L ^a   Vercauteren, D P ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

Critical points; Electron density; Medium resolution; Reduced representations; Solvent accessible surface area; Topological analysis

Indexed keywords

CARRIER CONCENTRATION; COMPLEXATION; COMPUTATIONAL METHODS; CRYSTALLOGRAPHY; INTERFACES (MATERIALS); MACROMOLECULES; OPTICAL RESOLVING POWER; SOLVENTS; SURFACE CHEMISTRY; TOPOLOGY;

CRITICAL POINTS (CP); MEDIUM RESOLUTION; REDUCED REPRESENTATIONS; SOLVENT ACCESSIBLE SURFACE AREA; TOPOLOGICAL ANALYSIS;

PROTEINS;

PROTEIN; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; ELECTRON; EVALUATION;

ELECTRONS; MODELS, MOLECULAR; PROTEINS; SOLVENTS;

EID: 2942588638     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20033     Document Type: Article

References (30)

1. Leherte, L.; Allen, F. H. J Comput Aided Mol Des 1994, 8, 257.
2. Leherte, L.; Fortier, S.; Glasgow, J.; Allen, F. H. Acta Crystallogr D 1994, 50, 155.
3. Leherte, L.; Glasgow, J.; Baxter, K.; Steeg, E.; Fortier, S. J Art Intell Res 1997, 7, 125.
4. Becue, A.; Meurice, N.; Leherte, L.; Vercauteren, D. P. Acta Crystallogr D 2003, 59, 2150.
5. Levitt, M. J Mol Biol 1976, 104, 59.
6. Wallqvist, A.; Ullner, M. Proteins: Struct Funct Genet 1994, 18, 267.
7. Hassinen, T.; Peräkylä, M. J Comput Chem 2001, 22, 1229.
8. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379.
9. Wang, Y. H.; Zhang, H.; Scott, R. A. Protein Sci 1995, 4, 1402.
10. Seidl, T.; Kriegel, H.-P. Proc Int Conf Intell Syst Mol Biol 1995, 3, 350.
11. Pan, X.; Bott, R.; Glatz, C. E. J Crystallogr Growth 2003, 254, 492.
12. Tüchsen, E.; Jensen, M. Ø. Westh, P. Chem Phys Lipids 2003, 123, 107.
13. Shrake, A.; Rupley, J. A. J Mol Biol 1973, 79, 351.
14. LeGrand, S. M.; Merz, K. M., Jr. J Comput Chem 1993, 14, 349.
15. Connolly, M. L. J Appl Crystallogr 1983, 16, 548.
16. Connolly, M. L. Science 1983, 221, 709.
17. Richmond, T. J. J Mol Biol 1984, 178, 63.
18. von Freyberg, B.; Richmond, T. J.; Braun, W. J Mol Biol 1993, 233, 275.
19. Gogonea, V.; Osawa, E. J Comput Chem 1995, 16, 817.
20. Fraczkiewicz, R.; Braun, W. J Comput Chem 1998, 19, 319.
21. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235-242.
22. [IBM] IBM Visualization Data Explorer (IBM Corporation, 1996); http://www.research.ibm.com/dx [WWW1] http://www.biochem.arizona.edu/classes/ bioc568/rasmletc.htm.
23. Hall, S. R.; du Boulay, D. J.; Olthof-Hazekamp, R. Xta13.7 System, 2000, University of Western Australia.
24. Leherte, L.; Latour, T.; Vercauteren, D. P. J Comput Aided Mol Des 1996, 10, 55.
25. Johnson, C. K. ORCRIT. The Oak Ridge Critical Point Network Program, 1977, Chemistry Division, Oak Ridge National Laboratory, NC.
26. Pedretti, A.; Villa, L.; Vistoli, G. J Mol Graphics Model 2002, 21, 47.
27. Chothia, C. Nature 1975, 254, 304.
28. Harpaz, Y.; Gerstein, M.; Chothia, C. Structure 1994, 2, 641.
29. Pontius, J.; Richelle, J.; Wodak, S. J. J Mol Biol 1996, 264, 121.
30. Tsai, J.; Taylor, R.; Chothia, C.; Gerstein, M. J Mol Biol 1999, 290, 253.