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BMC Bioinformatics. 2015 Jul 31;16:243. doi: 10.1186/s12859-015-0672-3.

Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.

Author information

1
Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. tatsiana.bylund@gmail.com.
2
United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tatsiana.bylund@gmail.com.
3
Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. aruvinsky@yahoo.com.
4
Schrödinger, Inc., Cambridge, MA, 02142, USA. aruvinsky@yahoo.com.
5
Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. deepkumar1983@gmail.com.
6
United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tuzikov@newman.bas-net.by.
7
Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. pkundro@ku.edu.
8
Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. vakser@ku.edu.
9
Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA. vakser@ku.edu.

Abstract

BACKGROUND:

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.

PMID:
26227548
PMCID:
PMC4521349
DOI:
10.1186/s12859-015-0672-3
[Indexed for MEDLINE]
Free PMC Article

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