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PRUNE and PROBE-two modular web services for protein-protein docking

Mitra, Pralay and Pal, Debnath (2011) PRUNE and PROBE-two modular web services for protein-protein docking. In: Nucleic Acids Research, 39 (2). W229-W234.

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Abstract

The protein-protein docking programs typically perform four major tasks: (i) generation of docking poses, (ii) selecting a subset of poses, (iii) their structural refinement and (iv) scoring, ranking for the final assessment of the true quaternary structure. Although the tasks can be integrated or performed in a serial order, they are by nature modular, allowing an opportunity to substitute one algorithm with another. We have implemented two modular web services, (i) PRUNE: to select a subset of docking poses generated during sampling search (http://pallab.serc.iisc.ernet.in/prune) and (ii) PROBE: to refine, score and rank them (http://pallab.serc.iisc.ernet.in/probe). The former uses a new interface area based edge-scoring function to eliminate > 95% of the poses generated during docking search. In contrast to other multi-parameter-based screening functions, this single parameter based elimination reduces the computational time significantly, in addition to increasing the chances of selecting native-like models in the top rank list. The PROBE server performs ranking of pruned poses, after structure refinement and scoring using a regression model for geometric compatibility, and normalized interaction energy. While web-service similar to PROBE is infrequent, no web-service akin to PRUNE has been described before. Both the servers are publicly accessible and free for use.

Item Type: Journal Article
Additional Information: Copyright of this article belongs to Oxford University Press.
Department/Centre: Division of Information Sciences > BioInformatics Centre
Division of Information Sciences > Supercomputer Education & Research Centre
Date Deposited: 18 Jul 2011 07:27
Last Modified: 18 Jul 2011 07:27
URI: http://eprints.iisc.ernet.in/id/eprint/39189

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