A simple shape characteristic of protein - Protein recognition

Bioinformatics

Volumn 23, Issue 7, 2007, Pages 789-792

  Nicola, George ^a   Vakser, Ilya A ^b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ANISOTROPY; ARTICLE; BINDING SITE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTALLIZATION; DATA BASE; MOLECULAR DOCKING; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; ALGORITHM; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SEQUENCE ANALYSIS; ULTRASTRUCTURE;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 34248579768     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm018     Document Type: Article

References (30)

1. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
2. Binkowski,T.A. et al. (2005) Protein surface analysis for function annotation in high-throughput structural genomics pipeline. Protein Sci., 14, 2972-2981.
3. del Sol,A. et al. (2006) Residue centrality, functionally important residues, and active site shape: Analysis of enzyme and non-enzyme families. Protein Sci., 15, 2120-2128.
4. Douguet,D. et al. (2006) DOCKGROUND resource for studying protein-protein interfaces. Bioinformatics, 22, 2612-2618.
5. Foote,J. and Raman,A. (2000) A relation between the principal axes of inertia and ligand binding. Proc. Natl. Acad. Sci. USA, 97, 978-983.
6. Glaser,F. et al. (2003) ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164.
7. Glaser,F. et al. (2001) Residue frequencies and pairing preferences at protein-protein interfaces. Proteins, 43, 89-102.
8. Gray,J.J. (2006) High-resolution protein-protein docking. Curr. Opin. Struct. Biol., 16, 183-193.
9. Gray,J.J. et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol., 331, 281-299.
10. Ho,C.M.W. and Marshall,G.R. (1990) Cavity search: An algorithm for the isolation and display of cavity-like binding regions. J. Comput. Aided Mol. Des., 4, 337-354.
11. Katchalski-Katzir,E. et al. (1992) Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. USA, 89, 2195-2199.
12. Keskin,O. et al. (2004) A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications. Protein Sci., 13, 1043-1055.
13. Larsen,T.A. et al. (1998) Morphology of protein-protein interfaces. Structure, 6, 421-427.
14. Lijnzaad,P. and Argos,P. (1997) Hydrophobic patches on protein subunit interfaces: Charactersitics and prediction. Proteins, 28, 333-343.
15. Marshall,G.R. and Vakser,I.A. (2005) Protein-protein docking methods. In Waksman,G. (ed.) Proteomics and Protein-Protein Interaction: Biology, Chemistry, Bioinformatics, and Drug Design. Springer, New York, pp. 115-146.
16. Nayal,M. and Honig,B. (2006) On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites. Proteins, 63, 892-906.
17. Novotny,J. et al. (1986) Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains). Proc. Natl. Acad. Sci. USA, 83, 226-230.
18. Ofran,Y. and Rost,B. (2003) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.
19. Papoian,G.A. and Wolynes,P.G. (2003) The physics and bioinformatics of binding and folding - an energy landscape perspective. Biopolymers 68, 333-349.
20. Pazos,F. and Sternberg,M.J.E. (2004) Automated prediction of protein function and detection of functional sites from structure. Proc. Natl. Acad. Sci. USA, 101, 14754-14759.
21. Rajamani,D. et al. (2004) Anchor residues in protein-protein interactions. Proc. Natl. Acad. Sci. USA, 101, 11287-11292.
22. Res,I. and Lichtarge,O. (2005) Character and evolution of protein-protein interfaces. Phys. Biol., 2, S36-S43.
23. Sali,A. and Blundell,T.L. (1993) Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
24. Szilagyi,A. et al. (2005) Prediction of physical protein-protein interactions. Phys. Biol., 2, S1-S16.
25. Tovchigrechko,A. and Vakser,I.A. (2001) How common is the funnel-like energy landscape in protein-protein interactions? Protein Sci., 10, 1572-1583.
26. Tovchigrechko,A. et al. (2002) Docking of protein models. Protein Sci., 11, 1888-1896.
27. Vajda,S. and Camacho,C.J. (2004) Protein-protein docking: Is the glass half-full or half-empty? Trends Biotechnol., 22, 110-116.
28. Vakser,I.A. et al. (1999) A systematic study of low-resolution recognition in protein-protein complexes. Proc. Natl. Acad. Sci. USA 96, 8477-8482.
29. Young,L. et al. (1994) A role for surface hydrophobicity in protein-protein recognition. Protein Sci., 3, 717-729.
30. Zhou,H.X. and Shan,Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44 336-343.