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

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TitleZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5.
Publication TypeJournal Article
Year of Publication2005
AuthorsWiehe, K, Pierce, BG, Mintseris, J, Tong, WWei, Anderson, R, Chen, R, Weng, Z
JournalProteins
Volume60
Issue2
Pagination207-13
Date Published2005 Aug 1
ISSN1097-0134
KeywordsAlgorithms, 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
Abstract

We present an evaluation of the results of our ZDOCK and RDOCK algorithms in Rounds 3, 4, and 5 of the protein docking challenge CAPRI. ZDOCK is a Fast Fourier Transform (FFT)-based, initial-stage rigid-body docking algorithm, and RDOCK is an energy minimization algorithm for refining and reranking ZDOCK results. Of the 9 targets for which we submitted predictions, we attained at least acceptable accuracy for 7, at least medium accuracy for 6, and high accuracy for 3. These results are evidence that ZDOCK in combination with RDOCK is capable of making accurate predictions on a diverse set of protein complexes.

DOI10.1002/prot.20559
Alternate JournalProteins
PubMed ID15981263