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Dockground: A comprehensive data resource for modeling of protein complexes
Author(s) -
Kundrotas Petras J.,
Anishchenko Ivan,
Dauzhenka Taras,
Kotthoff Ian,
Mnevets Daniil,
Copeland Matthew M.,
Vakser Ilya A.
Publication year - 2018
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3295
Subject(s) - docking (animal) , interactome , macromolecular docking , protein data bank (rcsb pdb) , decoy , computer science , protein–protein interaction , computational biology , protein–ligand docking , protein structure , protein data bank , bioinformatics , chemistry , biology , drug discovery , virtual screening , biochemistry , medicine , receptor , nursing , gene
Characterization of life processes at the molecular level requires structural details of protein interactions. The number of experimentally determined structures of protein-protein complexes accounts only for a fraction of known protein interactions. This gap in structural description of the interactome has to be bridged by modeling. An essential part of the development of structural modeling/docking techniques for protein interactions is databases of protein-protein complexes. They are necessary for studying protein interfaces, providing a knowledge base for docking algorithms, and developing intermolecular potentials, search procedures, and scoring functions. Development of protein-protein docking techniques requires thorough benchmarking of different parts of the docking protocols on carefully curated sets of protein-protein complexes. We present a comprehensive description of the Dockground resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2. The resource offers a variety of interconnected datasets of protein-protein complexes and other data for the development and testing of different aspects of protein docking methodologies. Based on protein-protein complexes extracted from the PDB biounit files, Dockground offers sets of X-ray unbound, simulated unbound, model, and docking decoy structures. All datasets are freely available for download, as a whole or selecting specific structures, through a user-friendly interface on one integrated website.