title: Simulated unbound structures for benchmarking of protein docking in the DOCKGROUND resource.
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.
authors.affiliation: Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. tatsiana.bylund@gmail.com.|United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tatsiana.bylund@gmail.com.
authors.forename: Tatsiana
authors.initials: T
authors.lastname: Kirys
authors.affiliation: Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. aruvinsky@yahoo.com.|Schrödinger, Inc., Cambridge, MA, 02142, USA. aruvinsky@yahoo.com.
authors.forename: Anatoly M
authors.initials: AM
authors.lastname: Ruvinsky
authors.affiliation: Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. deepkumar1983@gmail.com.
authors.forename: Deepak
authors.initials: D
authors.lastname: Singla
authors.affiliation: United Institute of Informatics Problems, National Academy of Sciences, 220012, Minsk, Belarus. tuzikov@newman.bas-net.by.
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Tuzikov
authors.affiliation: Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. pkundro@ku.edu.
authors.forename: Petras J
authors.initials: PJ
authors.lastname: Kundrotas
authors.affiliation: Center for Computational Biology, The University of Kansas, Lawrence, KS, 66047, USA. vakser@ku.edu.|Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, 66045, USA. vakser@ku.edu.
authors.forename: Ilya A
authors.initials: IA
authors.lastname: Vakser
mesh_terms: D000465:Algorithms; D019985:Benchmarking; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D020407:Internet; D062105:Molecular Docking Simulation; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D011506:Proteins