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Please use this identifier to cite or link to this item: https://elib.bsu.by/handle/123456789/259557
Title: Dockground: A comprehensive data resource for modeling of protein complexes
Authors: Kundrotas, P. J.
Anishchenko, I.
Dauzhenka, T.
Kotthoff, I.
Mnevets, D.
Copeland, M. M.
Vakser, I. A.
Issue Date: 2018
Publisher: Blackwell Publishing Ltd
Citation: Protein Sci 2018;27(1):172-181.
Abstract: 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resource (http://dockground.compbio.ku.edu) for structural modeling of protein interactions, including previously unpublished unbound docking benchmark set 4, and the X-ray docking decoy set 2.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.
URI: https://elib.bsu.by/handle/123456789/259557
Scopus: 10.1002/pro.3295
metadata.dc.identifier.scopus: 85039034079
Sponsorship: A number of people have contributed over the years to the development of Dockground. Dominique Douguet designed and generated the first bound database, Ying Gao built the original X-ray unbound sets, Shiyong Liu generated the first set of docking decoys, and Anatoly Ruvinsky and Tatsiana Kirys created the simulated unbound set, with the help of Deepak Singla. Andrey Tovchigrechko designed and implemented the original set of simulated protein models, which eventually led to the development of the Dockground current model–model sets. He also wrote GRAMM-X code used to build the original docking decoys.
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