HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets

Proteins: Structure, Function and Genetics

Volumn 69, Issue 4, 2007, Pages 726-733

  De Vries, Sjoerd J ^a   Van Dijk, Aalt D J ^a,c   Krzeminski, Mickaël ^a   Van Dijk, Mark ^a   Thureau, Aurelien ^a,d   Hsu, Victor ^b   Wassenaar, Tsjerk ^a   Bonvin, Alexandre M J J ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b OREGON STATE UNIVERSITY   (United States)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d CNRS   (France)

Author keywords

Flexible docking; HADDOCK; Multibody docking; Scoring

Indexed keywords

DOCKING PROTEIN;

COMPLEX FORMATION; CONFERENCE PAPER; METHODOLOGY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN TARGETING;

ALGORITHMS; AUTOMATION; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; GENOMICS; MODELS, STATISTICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; SOFTWARE;

EID: 36748998784     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21723     Document Type: Conference Paper

References (44)

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: Struct Funct Genet 2003;52:2-9.
2. Méndez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
3. Janin J. Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci 2005;14:278-283.
4. van Dijk AD, Boelens R, Bonvin AM. Data-driven docking for the study of biomolecular complexes. FEBS J 2005;272:293-312.
5. Bonvin AM. Flexible protein-protein docking. Curr Opin Struct Biol 2006;16:194-200.
6. van Dijk ADJ, de Vries SJ, Dominguez C, Chen H, Zhou HX, Bonvin AMJJ. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins: Struct Funct Bioinformatics 2005;60:232-238.
7. Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
8. Gray JJ. High-resolution protein-protein docking. Curr Opin Struct Biol 2006;16:183-193.
9. Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
10. Chen H, Zhou HX. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005;61:21-35.
11. de Vries SJ, van Dijk AD, Bonvin AM. WHISCY: what information does surface conservation yield? Application to data-driven docking. Proteins 2006;63:479-489.
12. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
13. Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
14. van Dijk M, van Dijk AD, Hsu V, Boelens R, Bonvin AM. Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility. Nucleic Acids Res 2006;34:3317-3325.
15. Wu AM, Singh T, Liu JH, Krzeminski M, Russwurm R, Siebert HC, Bonvin AM, Andre S, Gabius HJ. Activity-structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16. Glycobiology 2007;17:165-184.
16. van Dijk AD, Fushman D, Bonvin AM. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins 2005;60:367-381.
17. van Dijk AD, Kaptein R, Boelens R, Bonvin AM. Combining NMR relaxation with chemical shift perturbation data to drive protein-protein docking. J Biomol NMR 2006;34:237-244.
18. van Dijk AD, Bonvin AM. Solvated docking: introducing water into the modelling of biomolecular complexes. Bioinformatics 2006;22:2340-2347.
19. Nilges M, Gronenborn AM, Brunger AT, Clore GM. Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng 1988;2:27-38.
20. Fernandez-Recio J, Totrov M, Abagyan R. Identification of protein-protein interaction sites from docking energy landscapes. J Mol Biol 2004;335:843-865.
21. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 2003;374:461-491.
22. Kim DE, Chivian D, Baker D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 2004;32(Web Server issue):W526-W531.
23. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31:3381-3385.
24. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph 1990;8:52-56. 29.
25. Schuttelkopf AW, van Aalten DM. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 2004;60(Part 8):1355-1363.
26. Mendez 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.
27. Ghosh A, Praefcke GJ, Renault L, Wittinghofer A, Herrmann C. How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Nature 2006;440:101-104.
28. Graille M, Heurgue-Hamard V, Champ S, Mora L, Scrima N, Ulryck N, van Tilbeurgh H, Buckingham RH. Molecular basis for bacterial class I release factor methylation by PrmC. Mol Cell 2005;20:917-927.
29. Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by a natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
30. Hou Z, Bernstein DA, Fox CA, Keck JL. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
31. Menetrey J, Perderiset M, Cicolari J, Dubois T, Elkhatib N, El Khadali F, Franco M, Chavrier P, Houdusse A. Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes. EMBO J 2007;26:1953-1962.
32. Nielsen TK, Liu S, Luhrmann R, Ficner R. Structural basis for the bifunctionality of the U5 snRNP 52K protein (CD2BP2). J Mol Biol 2007;369:902-908.
33. Walker JR, Avvakumov GV, Xue S, Newman EM, Mackenzie F, Weigelt J, Sundstrom M, Arrowsmith CH, Edwards AM, Bochkarev A, Dhe-Paganon, S. A novel and unexpected complex between the SUMO-1-conjugating enzyme UBC9 and the ubiquitin-conjugating enzyme E2-25 kDa, to be published.
34. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
35. Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005;21:2534-2536.
36. 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.
37. 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.
38. Graille M, Stura EA, Bossus M, Muller BH, Letourneur O, Battail-Poirot N, Sibai G, Gauthier M, Rolland D, Le Du MH, Ducancel F. Crystal structure of the complex between the monomeric form of Toxoplasma gondii surface antigen 1 (SAG1) and a monoclonal antibody that mimics the human immune response. J Mol Biol 2005;354:447-458.
39. Terrak M, Kerff F, Langsetmo K, Tao T, Dominguez R. Structural basis of protein phosphatase 1 regulation. Nature 2004;429:780-784.
40. Graille M, Mora L, Buckingham RH, van Tilbeurgh H, de Zamaroczy M. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 2004;23:1474-1482.
41. 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.
42. 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.
43. Pichler A, Knipscheer P, Oberhofer E, van Dijk WJ, Korner R, Olsen JV, Jentsch S, Melchior F, Sixma TK. SUMO modification of the ubiquitin-conjugating enzyme E2-25K. Nat Struct Mol Biol 2005;12:264-269.
44. DeLano WL. The PyMOL Molecular Graphics System. Palo Alto, CA, USA: DeLano Scientific; 2002.