Structural templates for comparative protein docking

View/ Open
Issue Date
2015-09Author
Anishchenko, Ivan
Kundrotas, Petras J.
Tuzikov, Alexander V.
Vakser, Ilya A.
Publisher
Wiley
Type
Article
Article Version
Scholarly/refereed, author accepted manuscript
Rights
This is the peer reviewed version of the following article: Anishchenko, I., Kundrotas, P. J., Tuzikov, A. V. and Vakser, I. A. (2015), Structural templates for comparative protein docking. Proteins, 83: 1563–1570. doi:10.1002/prot.24736, which has been published in final form at http://doi.org/10.1002/prot.24736. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Metadata
Show full item recordAbstract
Structural characterization of protein-protein interactions is important for understanding life processes. Because of the inherent limitations of experimental techniques, such characterization requires computational approaches. Along with the traditional protein-protein docking (free search for a match between two proteins), comparative (template-based) modeling of protein-protein complexes has been gaining popularity. Its development puts an emphasis on full and partial structural similarity between the target protein monomers and the protein-protein complexes previously determined by experimental techniques (templates). The template-based docking relies on the quality and diversity of the template set. We present a carefully curated, non-redundant library of templates containing 4,950 full structures of binary complexes and 5,936 protein-protein interfaces extracted from the full structures at 12Å distance cut-off. Redundancy in the libraries was removed by clustering the PDB structures based on structural similarity. The value of the clustering threshold was determined from the analysis of the clusters and the docking performance on a benchmark set. High structural quality of the interfaces in the template and validation sets was achieved by automated procedures and manual curation. The library is included in the Dockground resource for molecular recognition studies at http://dockground.bioinformatics.ku.edu.
Collections
Citation
Anishchenko, I., Kundrotas, P. J., Tuzikov, A. V. and Vakser, I. A. (2015), Structural templates for comparative protein docking. Proteins, 83: 1563–1570. doi:10.1002/prot.24736
Items in KU ScholarWorks are protected by copyright, with all rights reserved, unless otherwise indicated.
We want to hear from you! Please share your stories about how Open Access to this item benefits YOU.