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dc.contributor.authorKirys, Tatsiana
dc.contributor.authorRuvinsky, Anatoly M.
dc.contributor.authorSingla, Deepak
dc.contributor.authorTuzikov, Alexander V.
dc.contributor.authorKundrotas, Petras J.
dc.contributor.authorVakser, Ilya A.
dc.date.accessioned2016-02-12T21:41:43Z
dc.date.available2016-02-12T21:41:43Z
dc.date.issued2015-07-31
dc.identifier.citationKirys, Tatsiana, Anatoly M. Ruvinsky, Deepak Singla, Alexander V. Tuzikov, Petras J. Kundrotas, and Ilya A. Vakser. "Simulated Unbound Structures for Benchmarking of Protein Docking in the Dockground Resource." BMC Bioinformatics 16.1 (2015): n. pag. doi:10.1186/s12859-015-0672-3.en_US
dc.identifier.urihttp://hdl.handle.net/1808/20064
dc.description.abstractBackground

Proteins play an important role in biological processes in living organisms. Many protein functions are based on interaction with other proteins. The structural information is important for adequate description of these interactions. Sets of protein structures determined in both bound and unbound states are essential for benchmarking of the docking procedures. However, the number of such proteins in PDB is relatively small. A radical expansion of such sets is possible if the unbound structures are computationally simulated.

Results

The dockground public resource provides data to improve our understanding of protein–protein interactions and to assist in the development of better tools for structural modeling of protein complexes, such as docking algorithms and scoring functions. A large set of simulated unbound protein structures was generated from the bound structures. The modeling protocol was based on 1 ns Langevin dynamics simulation. The simulated structures were validated on the ensemble of experimentally determined unbound and bound structures. The set is intended for large scale benchmarking of docking algorithms and scoring functions.

Conclusions

A radical expansion of the unbound protein docking benchmark set was achieved by simulating the unbound structures. The simulated unbound structures were selected according to criteria from systematic comparison of experimentally determined bound and unbound structures. The set is publicly available at http://dockground.compbio.ku.edu.
en_US
dc.publisherBioMed Centralen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0
dc.subjectProtein interactionsen_US
dc.subjectProtein dockingen_US
dc.subjectMolecular recognitionen_US
dc.subjectConformational analysisen_US
dc.titleSimulated unbound structures for benchmarking of protein docking in the dockground resourceen_US
dc.typeArticle
kusw.kuauthorKundrotas, Petras J.
kusw.kudepartmentComputational Biologyen_US
dc.identifier.doi10.1186/s12859-015-0672-3
kusw.oaversionScholarly/refereed, publisher version
kusw.oapolicyThis item meets KU Open Access policy criteria.
dc.rights.accessrightsopenAccess


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as: This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.