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Structural templates for comparative protein docking
dc.contributor.author | Anishchenko, Ivan | |
dc.contributor.author | Kundrotas, Petras J. | |
dc.contributor.author | Tuzikov, Alexander V. | |
dc.contributor.author | Vakser, Ilya A. | |
dc.date.accessioned | 2017-05-08T15:55:32Z | |
dc.date.available | 2017-05-08T15:55:32Z | |
dc.date.issued | 2015-09 | |
dc.identifier.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 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/23997 | |
dc.description.abstract | 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. | en_US |
dc.publisher | Wiley | en_US |
dc.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. | en_US |
dc.subject | Protein recognition | en_US |
dc.subject | Protein modeling | en_US |
dc.subject | Benchmark sets | en_US |
dc.subject | Structure prediction | en_US |
dc.subject | Protein interactions | en_US |
dc.title | Structural templates for comparative protein docking | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Anishchenko, Ivan | |
kusw.kuauthor | Kundrotas, Petras J. | |
kusw.kuauthor | Vakser, Ilya A. | |
kusw.kudepartment | Molecular Biosciences | en_US |
kusw.kudepartment | Center for Bioinformatics | en_US |
dc.identifier.doi | 10.1002/prot.24736 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0003-3645-2044 | |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.rights.accessrights | openAccess |