ZDOCK predictions for the CAPRI challenge

Proteins: Structure, Function and Genetics

Volumn 52, Issue 1, 2003, Pages 68-73

  Chen, Rong ^a   Tong, Weiwei ^b   Mintseris, Julian ^a   Li, Li ^a   Weng, Zhiping ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

Blind test; CAPRI; Desolvation; Electrostatics; Protein docking; Shape complementarity; ZDOCK

Indexed keywords

DOCKING PROTEIN; PROTEIN; PROTEIN KINASE; SUPERANTIGEN; T LYMPHOCYTE RECEPTOR BETA CHAIN;

ALGORITHM; ANTIGEN ANTIBODY COMPLEX; ARTICLE; COMPUTER PREDICTION; CRYSTAL STRUCTURE; ELECTRICITY; ENZYME SUBSTRATE COMPLEX; FOURIER TRANSFORMATION; PERFORMANCE; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SOLVATION; ZDOCK ALGORITHM;

ALGORITHMS; ALPHA-AMYLASE; ANIMALS; ANTIBODIES; ANTIGENS, VIRAL; BACTERIAL PROTEINS; BINDING SITES; CAPSID PROTEINS; EXOTOXINS; HEMAGGLUTININS; MACROMOLECULAR SUBSTANCES; MEMBRANE PROTEINS; MODELS, MOLECULAR; PHOSPHOENOLPYRUVATE SUGAR PHOSPHOTRANSFERASE SYSTEM; PROTEIN INTERACTION MAPPING; PROTEIN-SERINE-THREONINE KINASES; PROTEINS; RECEPTORS, ANTIGEN, T-CELL, ALPHA-BETA;

EID: 0037561868     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10388     Document Type: Article

References (27)

1. Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
2. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins. Forthcoming.
3. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein docking algorithm. Proteins 2003;52:80-87.
4. Chen R, Mintseris J, Janin J, Weng Z. A protein-protein docking benchmark. Proteins 2003;52:88-91.
5. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
6. Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
7. Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins 2000;39:178-194.
8. Gardiner EJ, Willett P, Artymiuk PJ. Protein docking using a genetic algorithm. Proteins 2001;44:44-56.
9. Zhu PP, Herzberg O, Peterkofsky A. Topography of the interaction of HPr(Ser) kinase with HPr. Biochemistry 1998;37:11762-11770.
10. Monedero V, Poncet S, Mijakovic I, Fieulaine S, Dossonnet V, Martin-Verstraete I, Nessler S, Deutscher J. Mutations lowering the phosphatase activity of HPr kinase/phosphatase switch off carbon metabolism. EMBO J 2001;20:3928-3937.
11. Audette GF, Engelmann R, Hengstenberg W, Deutscher J, Hayakawa K, Quail JW, Delbaere LT. The 1.9 A resolution structure of phospho-serine 46 HPr from Enterococcus faecalis. J Mol Biol 2000;303:545-553.
12. Fieulaine S, Morera S, Poncet S, Monedero V, Gueguen-Chaignon V, Galinier A, Janin J, Deutscher J, Nessler S. X-ray structure of HPr kinase: a bacterial protein kinase with a P-loop nucleotidebinding domain. EMBO J 2001;20:3917-3927.
13. Fieulaine S, Morera S, Poncet S, Mijakovic I, Galinier A, Janin J, Deutscher J, Nessler S. X-ray structure of a bifunctional protein kinase in complex with its protein substrate HPr. Proc Natl Acad Sci USA 2002;99:13437-13441.
14. Mathieu M, Petitpas I, Navaza J, Lepault J, Kohli E, Pothier P, Prasad BV, Cohen J, Rey FA. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J 2001;20:1485-1497.
15. Thouvenin E, Schoehn G, Rey F, Petitpas I, Mathieu M, Vaney MC, Cohen J, Kohli E, Pothier P, Hewat E. Antibody inhibition of the transcriptase activity of the rotavirus DLP: a structural view. J Mol Biol 2001;307:161-172.
16. Gigant B, Barbey-Martin C, Bizebard T, Fleury D, Daniels R, Skehel JJ, Knossow M. A neutralizing antibody Fab-influenza haemagglutinin complex with an unprecedented 2:1 stoichiometry: characterization and crystallization. Acta Crystallogr D Biol Crystallogr 2000;56:1067-1069.
17. Barbey-Martin C, Gigant B, Bizebard T, Calder LJ, Wharton SA, Skehel JJ, Knossow M. An antibody that prevents the hemagglutinin low pH fusogenic transition. Virology 2002;294:70-74.
18. Desmyter A, Decanniere K, Muyldermans S, Wyns L. Antigen specificity and high affinity binding provided by one single loop of a camel single-domain antibody. J Biol Chem 2001;276:26285-26290.
19. Desmyter A, Transue TR, Ghahroudi MA, Thi MH, Poortmans F, Hamers R, Muyldermans S, Wyns L. Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Nat Struct Biol 1996;3:803-811.
20. Decanniere K, Desmyter A, Lauwereys M, Ghahroudi MA, Muyldermans S, Wyns L. A single-domain antibody fragment in complex with RNase A: non-canonical loop structures and nanomolar affinity using two CDR loops. Structure Fold Des 1999;7:361-370.
21. Lauwereys M, Arbabi Ghahroudi M, Desmyter A, Kinne J, Holzer W, De Genst E, Wyns L, Muyldermans S. Potent enzyme inhibitors derived from dromedary heavy-chain antibodies. EMBO J 1998;17:3512-3520.
22. Li H, Llera A, Tsuchiya D, Leder L, Ysern X, Schlievert PM, Karjalainen K, Mariuzza RA. Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B. Immunity 1998;9:807-816.
23. Sundberg EJ, Li Y, Mariuzza RA. So many ways of getting in the way: diversity in the molecular architecture of superantigendependent T-cell signaling complexes. Curr Opin Immunol 2002;14:36-44.
24. Fields BA, Malchiodi EL, Li H, Ysern X, Stauffacher CV, Schlievert PM, Karjalainen K, Mariuzza RA. Crystal structure of a T-cell receptor beta-chain complexed with a superantigen. Nature 1996;384:188-192.
25. Papageorgiou AC, Collins CM, Gutman DM, Kline JB, O'Brien SM, Tranter HS, Acharya KR. Structural basis for the recognition of superantigen streptococcal pyrogenic exotoxin A (SpeA1) by MHC class II molecules and T-cell receptors. EMBO J 1999;18:9-21.
26. Sundberg EJ, Li H, Llera AS, McCormick JK, Tormo J, Schlievert PM, Karjalainen K, Mariuzza RA. Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes. Structure (Camb) 2002;10:687-699.
27. DeLano WL. The PyMOL Molecular Graphics System on World Wide Web. 2002.