Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?
dc.contributor.author | Sinha, Rohita | |
dc.contributor.author | Kundrotas, Petras J. | |
dc.contributor.author | Vakser, Ilya A. | |
dc.date.accessioned | 2014-03-20T14:24:17Z | |
dc.date.available | 2014-03-20T14:24:17Z | |
dc.date.issued | 2012-02-13 | |
dc.identifier.citation | Sinha, R., Kundrotas, P. J., & Vakser, I. A. (2012). Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed? PLoS ONE, 7(2). http://dx.doi.org/10.1371/journal.pone.0031349 | |
dc.identifier.uri | http://hdl.handle.net/1808/13284 | |
dc.description.abstract | The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures. | |
dc.description.sponsorship | This work was supported by National Institutes of Health grant R01 GM074255. | |
dc.publisher | Public Library of Science | |
dc.rights | ©2012 Sinha et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Cytokine receptors | |
dc.subject | Cytokine | |
dc.subject | Enzyme structure | |
dc.subject | Hormones | |
dc.subject | Protein structure | |
dc.subject | Protein structure comparison | |
dc.subject | Sequence alignment | |
dc.title | Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed? | |
dc.type | Article | |
kusw.kuauthor | Sinha, Rohita | |
kusw.kuauthor | Kundrotas, Petras J. | |
kusw.kuauthor | Vakser, Ilya A. | |
kusw.kudepartment | Molecular Biosciences | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1371/journal.pone.0031349 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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Except where otherwise noted, this item's license is described as: ©2012 Sinha et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.