ZDOCK predictions for the CAPRI challenge - PubMed (original) (raw)
. 2003 Jul 1;52(1):68-73.
doi: 10.1002/prot.10388.
Affiliations
- PMID: 12784369
- DOI: 10.1002/prot.10388
ZDOCK predictions for the CAPRI challenge
Rong Chen et al. Proteins. 2003.
Abstract
The CAPRI Challenge is a blind test of protein-protein-docking algorithms that predict the complex structure from the crystal structures of the interacting proteins. We participated in both rounds of this blind test and submitted predictions for all seven targets, relying mainly on our Fast Fourier Transform based algorithm ZDOCK that combines shape complementarity, desolvation, and electrostatics. Our group made good predictions for three targets and had at least some success with three others. Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed.
Copyright 2003 Wiley-Liss, Inc.
Similar articles
- Assessment of blind predictions of protein-protein interactions: current status of docking methods.
Méndez R, Leplae R, De Maria L, Wodak SJ. Méndez R, et al. Proteins. 2003 Jul 1;52(1):51-67. doi: 10.1002/prot.10393. Proteins. 2003. PMID: 12784368 - Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information.
Law DS, Ten Eyck LF, Katzenelson O, Tsigelny I, Roberts VA, Pique ME, Mitchell JC. Law DS, et al. Proteins. 2003 Jul 1;52(1):33-40. doi: 10.1002/prot.10395. Proteins. 2003. PMID: 12784365 - Successful discrimination of protein interactions.
Camacho CJ, Gatchell DW. Camacho CJ, et al. Proteins. 2003 Jul 1;52(1):92-7. doi: 10.1002/prot.10394. Proteins. 2003. PMID: 12784373 - Protein-protein docking tested in blind predictions: the CAPRI experiment.
Janin J. Janin J. Mol Biosyst. 2010 Dec;6(12):2351-62. doi: 10.1039/c005060c. Epub 2010 Aug 19. Mol Biosyst. 2010. PMID: 20725658 Review. - Three-dimensional structures of protein-protein complexes in the E. coli PTS.
Peterkofsky A, Wang G, Garrett DS, Lee BR, Seok YJ, Clore GM. Peterkofsky A, et al. J Mol Microbiol Biotechnol. 2001 Jul;3(3):347-54. J Mol Microbiol Biotechnol. 2001. PMID: 11361064 Review.
Cited by
- Performance of ZDOCK and IRAD in CAPRI rounds 28-34.
Vreven T, Pierce BG, Borrman TM, Weng Z. Vreven T, et al. Proteins. 2017 Mar;85(3):408-416. doi: 10.1002/prot.25186. Epub 2016 Oct 24. Proteins. 2017. PMID: 27718275 Free PMC article. - The development of an affinity evaluation and prediction system by using protein-protein docking simulations and parameter tuning.
Tsukamoto K, Yoshikawa T, Yokota K, Hourai Y, Fukui K. Tsukamoto K, et al. Adv Appl Bioinform Chem. 2009;2:1-15. doi: 10.2147/aabc.s3646. Epub 2009 Jan 12. Adv Appl Bioinform Chem. 2009. PMID: 21918611 Free PMC article. - Identification and rational redesign of peptide ligands to CRIP1, a novel biomarker for cancers.
Hao J, Serohijos AW, Newton G, Tassone G, Wang Z, Sgroi DC, Dokholyan NV, Basilion JP. Hao J, et al. PLoS Comput Biol. 2008 Aug 1;4(8):e1000138. doi: 10.1371/journal.pcbi.1000138. PLoS Comput Biol. 2008. PMID: 18670594 Free PMC article. - In silico protein function prediction: the rise of machine learning-based approaches.
Chen J, Gu Z, Lai L, Pei J. Chen J, et al. Med Rev (2021). 2023 Nov 29;3(6):487-510. doi: 10.1515/mr-2023-0038. eCollection 2023 Dec. Med Rev (2021). 2023. PMID: 38282798 Free PMC article. Review. - Iron-sulfur cluster biosynthesis: characterization of IscU-IscS complex formation and a structural model for sulfide delivery to the [2Fe-2S] assembly site.
Nuth M, Cowan JA. Nuth M, et al. J Biol Inorg Chem. 2009 Aug;14(6):829-39. doi: 10.1007/s00775-009-0495-7. Epub 2009 Mar 24. J Biol Inorg Chem. 2009. PMID: 19308466
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources