Approaching the CAPRI challenge with an efficient geometry-based docking

Proteins: Structure, Function and Genetics

Volumn 60, Issue 2, 2005, Pages 217-223

  Inbar, Yuval ^a   Schneidman Duhovny, Dina ^a   Halperin, Inbal ^a   Oron, Assaf ^a   Nussinov, Ruth ^a,b   Wolfson, Haim J ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b SAIC FREDERICK INC   (United States)

Author keywords

CAPRI; FlexDock; Flexible docking; PatchDock; SymmDock; Symmetry docking; Unbound docking

Indexed keywords

ALGORITHM; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; EXPERIMENT; FLEXDOCK ALGORITHM; GENOMICS; GEOMETRY; MOLECULAR DYNAMICS; PATCHDOCK ALGORITHM; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RETROSPECTIVE STUDY; RIGIDITY; SEQUENCE HOMOLOGY; SYMMDOCK ALGORITHM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; DIMERIZATION; ELECTROSTATICS; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MODELS, THEORETICAL; MOLECULAR CONFORMATION; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 21644438254     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20561     Document Type: Conference Paper

References (30)

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. Zhang C, Vasmatzis G, Cornette JL. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997;267:707-726.
3. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ Geometry-based flexible and symmetric protein docking. Proteins 2005;60:224-231.
4. Takagi J, Yang Y, Liu JH, Wang JH, Springer TA. Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface. Nature 2003;424:969-974.
5. Stetefeld J, Mayer U, Timpl R, Huber R. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gammal chain harboring the nidogen binding site J Mol Biol 1996;257:644-657.
6. Springer TA. An extracellular beta-propeller module predicted in lipoprotein and scavenger receptors, tyrosine kinases, epidermal growth factor precursor, and extracellular matrix components. J Mol Biol 1998;283:837-862.
7. Graille M, Zhou CZ, Receveur V, Collinet B, Declerck N, van Tilbeurgh H. Structure of the native and inactive LicT PRD from B. subtilis. J Biol Chem 2005;280(15):14780-14789.
8. Méndez R, Wodak SJ. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
9. van Tilbeurgh H, Le Coq D, Declerck N. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. EMBO J 2001;20:3789-3799.
10. Goodsell DS, Olson AJ. Structural symmetry and protein function. Annu Rev Biophys Biomol Struct 2000;29:105-153.
11. Shatsky M, Nussinov R, Wolfson HJ. Flexible protein alignment and hinge detection. Proteins 2002;48:242-256. Available online at http://bioinfo3d.cs. tau.ac.il/FlexProt.
12. 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.
13. Gibbons DL, Vaney MC, Roussel A, Vigouroux A, Reilly B, Lepault J, Kielian M, Rey FA. Conformational change and protein-protein interactions of the fusion protein of semliki forest virus. Nature 2004;427:320-325.
14. Rey FA, Heinz FX, Mandl C, Kunz C, Harrison SC. The envelope glycoprotein from tick-borne encephalitis virus at 2Å resolution. Nature 1995;375:291-298.
15. Allison SL, Schalich J, Stiasny K, Mandl CW, Heinz FX. Mutational evidence for an internal fusion peptide in flavivirus envelope protein E. J Virol 2001;75:4268-4275.
16. Carvalho AL, Dias FMV, Prates JAM, Nagy T, Gilbert HJ, Davies GJ, Ferreira LMA, Romao MJ, Fontes CMGA. Cellulosome assembly revealed by the crystal structure of the cohesin-dockerin complex. Proc Natl Acad Sci USA 2003;100:13809-13814.
17. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
18. Leibovitz E, Beguin PA. A new type of cohesin domain that specifically binds the dockerin domain of the Clostridium thermoccelum scaffolding dockerin binding protein SbdA. J Bacteriol 1996;178:1200-1203.
19. Tavares GA, Beguin P, Alzari PM. The crystal structure of a type I cohesin domain at 1.7Å resolution. J Mol Biol 1997;273:701-713.
20. He XL, Grigg ME, Boothroyd JC, Garcia KC. Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily. Nat Struct Biol 2002;9:606-611.
21. Camacho CJ, Gatchell D. Successful discrimination of protein interactions. Proteins 2003;52:92-97.
22. Toth A, Kiss E, Herberg FW, Gergely P, Hartshorne DJ, Erdodi F. Study of the subunit interactions in myosin phosphatase by surface plasmon resonance. Eur J Biochem 2000;267:1687-1697.
23. Egloff MP, Johnson DF, Moorhead G, Cohen PT, Cohen P, Barford D. Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1. EMBO J 1997;16: 1876-1887.
24. Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
25. Krengel U, Dijkstra BW. Three-dimensional structure of endo-1,4-beta-xylanase i from Aspergillus niger: molecular basis for its low pH optimum. J Mol Biol 1996;263:70-78.
26. Tahir TA, Berrin JG, Flatman R, Roussel A, Roepstorff P, Williamson G, Juge N. Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger. J Biol Chem 2002;277:44035-44043.
27. 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.
28. Dominguez C, Boelens R, Bonvin A. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
29. Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
30. Gray JJ, Moughan S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.