ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5

Proteins: Structure, Function and Genetics

Volumn 60, Issue 2, 2005, Pages 207-213

  Wiehe, Kevin ^a   Pierce, Brian ^a   Mintseris, Julian ^a   Tong, Wei Wei ^b   Anderson, Robert ^a   Chen, Rong ^a   Weng, Zhiping ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

Blind test; CAPRI; Protein docking; RDOCK; Scoring function; ZDOCK

Indexed keywords

ACCURACY; ALGORITHM; COMPLEX FORMATION; CONFERENCE PAPER; ENERGY; EVALUATION; FOURIER TRANSFORMATION; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RDOCK ALGORITHM; RIGIDITY; SCORING SYSTEM; ZDOCK ALGORITHM;

ALGORITHMS; ANIMALS; BINDING SITES; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; DIMERIZATION; HUMANS; INTERNET; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 21644470603     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20559     Document Type: Conference Paper

References (39)

1. Janin J, Henrick K, Moult J, Ten Eyck L, Sternberg MJE, Vajda S, Vasker I, Wodak SJ. CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 2003;52:2-9.
2. 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.
3. Chen R, Tong WW, Mintseris J, Li L, Weng ZP. ZDOCK predictions for the CAPRI challenge. Proteins 2003;52:68-73.
4. Chen R, Weng ZP. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
5. Chen R, Weng ZP. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
6. Chen R, Mintseris J, Janin J, Weng ZP. A protein-protein docking benchmark. Proteins 2003;52:88-91.
7. Mintseris J, Wiehe K, Pierce B, Anderson RJ, Chen R, Janin J, Weng Z. Protein-Protein Docking Benchmark 2.0: an update. Proteins 2005;60:214-216.
8. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
9. Li L, Chen R, Weng ZP. RDOCK: Refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
10. Chen R, Weng Z. A novel shape complementarity scoring function for protein-protein docking. Proteins 2003;51:397-408.
11. Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
12. n symmetric multimer docking. Bioinformatics 2005;21:1472-1478.
13. Poschl E, Mayer U, Stetefeld J, Baumgartner R, Holak TA, Huber R, Timpl R. Site-directed mutagenesis and structural interpretation of the nidogen binding site of the laminin gamma1 chain. EMBO J 1996;15:5154-5159.
14. DeLano WL. The PyMOL molecular graphics system. San Carlos, CA: DeLano Scientific; 2002.
15. 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.
16. Bower MJ, Cohen FE, Dunbrack RL Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
17. Mintseris J, Weng Z. Atomic contact vectors in protein-protein recognition. Proteins 2003;53:629-639.
18. 17a. Graille M, Zhou CZ, Receveur-Brechot V, Collinet B, Declerck N, van Tilbeurgh H. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J Biol Chem 2005;280:14780-14789. PMID: 15699035.
19. 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.
20. Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F. A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly. Structure 1997;5:381-390.
21. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31:3381-3385.
22. Mechaly A, Yaron S, Lamed R, Fierobe HP, Belaich A, Belaich JP, Shoham Y, Bayer EA. Cohesin-dockerin recognition in cellulosome assembly: experiment versus hypothesis. Proteins 2000;39: 170-177.
23. Mechaly A, Fierobe HP, Belaich A, Belaich JP, Lamed R, Shoham Y, Bayer EA. Cohesin-dockerin interaction in cellulosome assembly: a single hydroxyl group of a dockerin domain distinguishes between nonrecognition and high affinity recognition. J Biol Chem 2001;276:9883-9888.
24. Miras I, Schaeffer F, Beguin P, Alzari PM. Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA. Biochemistry 2002;41:2115-2119.
25. 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.
26. Goldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J. Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 1995;376:745-753.
27. Tanaka J, Ito M, Feng J, Ichikawa K, Hamaguchi T, Nakamura M, Hartshorne DJ, Nakano T. Interaction of myosin phosphatase target subunit 1 with the catalytic subunit of type 1 protein phosphatase. Biochemistry 1998;37:16697-16703.
28. Hirano K, Phan BC, Hartshorne DJ. Interactions of the subunits of smooth muscle myosin phosphatase. J Biol Chem 1997;272: 3683-3688.
29. Zhao S, Lee EY. A protein phosphatase-1-binding motif identified by the panning of a random peptide display library. J Biol Chem 1997;272:28368-28372.
30. 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.
31. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
32. 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.
33. Furniss CS, Belshaw NJ, Alcocer MJ, Williamson G, Elliott GO, Gebruers K, Haigh NP, Fish NM, Kroon PA. A family 11 xylanase from Penicillium funiculosum is strongly inhibited by three wheat xylanase inhibitors. Biochim Biophys Acta 2002;1598:24-29.
34. Bray MR, Clarke AJ. Identification of a glutamate residue at the active site of xylanase A from Schizophyllum commune. Eur J Biochem 1994;219:821-827.
35. Ko EP, Akatsuka H, Moriyama H, Shinmyo A, Hata Y, Katsube Y, Urabe I, Okada H. Site-directed mutagenesis at aspartate and glutamate residues of xylanase from Bacillus pumilus. Biochem J 1992;288:117-121.
36. Wakarchuk WW, Campbell RL, Sung WL, Davoodi J, Yaguchi M. Mutational and crystallographic analyses of the active site residues of the Bacillus circulans xylanase. Protein Sci 1994;3:467-475.
37. Miao S, Ziser L, Aebersold R, Withers SG. Identification of glutamic acid 78 as the active site nucleophile in Bacillus subtilis xylanase using electrospray tandem mass spectrometry. Biochemistry 1994;33:7027-7032.
38. 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 aestiuum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
39. 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.