DockYard-a repository to assist modeling of protein-protein docking

Mitra, Pralay and Pal, Debnath (2011) DockYard-a repository to assist modeling of protein-protein docking. In: Journal of Molecular Modeling, 17 (3). pp. 599-606.

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Abstract

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Item Type:	Journal Article
Publication:	Journal of Molecular Modeling
Publisher:	Springer
Additional Information:	Copyright of this article belongs to Springer.
Keywords:	Decoy;Docking;Interaction;Interlogs;Protein-protein; Repository
Department/Centre:	Division of Information Sciences (Doesn't exist now) > BioInformatics Centre Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited:	06 May 2011 06:06
Last Modified:	06 May 2011 10:33
URI:	http://eprints.iisc.ac.in/id/eprint/37380

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