Protein–Protein Docking: Overview and Performance Analysis

Bioinformatics Program, Boston University, Boston, MA, USA.
Methods in Molecular Biology (Impact Factor: 1.29). 02/2008; 413:283-314. DOI: 10.1007/978-1-59745-574-9_11
Source: PubMed

ABSTRACT 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.

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    • "Fast Fourier Transform (FFT) algorithm was applied to perform a global docking to search for potential binding positions of two component proteins (Pierce et al., 2014). Since validity of the ZDOCK analysis is affected by the accuracy of the search algorithm as well as the proteinprotein complex to be predicted, some of the top-scoring predictions resulted from the soft scoring function of the program could be false positives (Wiehe et al., 2008). Combining the results from epitope prediction softwares based on mimotope and ZDOCK may lead to a more reliable result. "
    Protein & Cell 11/2014; 5(12). DOI:10.1007/s13238-014-0115-3 · 2.85 Impact Factor
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    • "Qualitative protein function annotation using Enzyme Commission (EC) numbers or Gene Ontology (Ashburner et al., 2000) terms is typically followed by a comprehensive functional characterization at the molecular level. The studies of interactions between proteins and other molecular species in a cell are routinely supported by computations involving docking of DNA (Gao and Skolnick, 2009; van Dijk and Bonvin, 2008), other protein partners (Lyskov and Gray, 2008; Wiehe et al., 2008) and small ligands (Goodsell et al., 1996; Moustakas et al., 2006). In the latter case, the docking of specific ligands can be extended to large-scale virtual screening of combinatorial libraries in order to discover novel bioactive compounds (Rajamani and Good, 2007; Seifert et al., 2007). "
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