Improving CAPRI predictions: Optimized desolvation for rigid-body docking

Proteins: Structure, Function and Genetics

Volumn 60, Issue 2, 2005, Pages 308-313

  Fernández Recio, Juan ^a,d   Abagyan, Ruben ^b   Totrov, Maxim ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

^c MOLSOFT LLC   (United States)

^d INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

OCTANOL; WATER;

ACCURACY; AMINO ACID SEQUENCE; ANTIGEN ANTIBODY COMPLEX; AUTOMATION; CONFERENCE PAPER; DESOLVATION; EXPERIMENT; GEOMETRY; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; RIGIDITY; SCORING SYSTEM; SEQUENCE HOMOLOGY; SOLVATION;

ALGORITHMS; ANIMALS; BACTERIAL PROTEINS; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; DIMERIZATION; ELECTROSTATICS; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 21644447570     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20575     Document Type: Conference Paper

References (21)

1. Méndez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
2. Fernández-Recio J, Totrov M, Abagyan R. ICM-DISCO docking by global energy optimization with fully flexible side-chains. Proteins 2003;52:113-117.
3. Conte LL, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
4. Norel R, Petrey D, Wolfson HJ, Nussinov R. Examination of shape complementarity in docking of unbound proteins. Proteins 1999;36: 307-317.
5. Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes. Proc Natl Acad Sci USA 1999;96:8477-8482.
6. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
7. Abagyan R, Totrov M, Kuznetsov D. ICM-a new method for structure modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comp Chem 1994;15:488-506.
8. Totrov M, Abagyan R. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nat Struct Biol 1994;1:259-263.
9. Fernández-Recio J, Totrov, M., Abagyan, R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
10. Fernández-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
11. Fernández-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 2005;58:134-143.
12. Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
13. Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997;Suppl 1:215-220.
14. Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-857.
15. Totrov M, Abagyan R. Protein-ligand docking as an energy optimization problem. In: Raffa RB, Editor. Drug-receptor thermodynamics: introduction and applications. New York: Wiley; 2001. p 603-624.
16. Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
17. Abagyan R, Argos P. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J Mol Biol 1992;225:519-532.
18. Bressanelli S, Stiasny K, Allison SL, Stura EA, Duquerroy S, Lescar J, Heinz FX, Rey FA. Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO J 2004;23:728-738.
19. Carvalho AL, Dias FM, Prates JA, Nagy T, Gilbert HJ, Davies GJ, Ferreira LM, Romao MJ, Fontes CM. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
20. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
21. Eghiaian F, Grosclaude J, Lesceu S, Debey P, Doublet B, Treguer E, Rezaei H, Knossow M. Insight into the PrPC→PrPSc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants. Proc Natl Acad Sci USA 2004;101:10254-10259.