Protein-protein docking: overview and performance analysis.

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TitleProtein-protein docking: overview and performance analysis.
Publication TypeJournal Article
Year of Publication2008
AuthorsWiehe, K, Peterson, MW, Pierce, BG, Mintseris, J, Weng, Z
JournalMethods Mol Biol
Date Published2008
KeywordsAlgorithms, Animals, Binding Sites, Databases, Protein, Humans, Models, Molecular, Multiprotein Complexes, Protein Conformation, Protein Folding, Protein Interaction Mapping, Software

Protein-protein docking is the computational prediction of protein complex structure given the individually solved component protein structures. It is an important means for understanding the physicochemical forces that underlie macromolecular interactions and a valuable tool for modeling protein complex structures. Here, we report an overview of protein-protein docking with specific emphasis on our Fast Fourier Transform-based rigid-body docking program ZDOCK, which is consistently rated as one of the most accurate docking programs in the Critical Assessment of Predicted Interactions (CAPRI), a series of community-wide blind tests. We also investigate ZDOCK's performance on a non-redundant protein complex benchmark. Finally, we perform regression analysis to better understand the strengths and weaknesses of ZDOCK and to suggest areas of future development for protein-docking algorithms in general.

Alternate JournalMethods Mol. Biol.
PubMed ID18075170