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This article is part of the supplement: Italian Society of Bioinformatics (BITS): Annual Meeting 2011

Open Access Research

CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions

Anna Vangone1, Romina Oliva2* and Luigi Cavallo1

Author Affiliations

1 Department of Chemistry and Biology, University of Salerno, Via Ponte Don Melillo, Fisciano (SA), 84084, Italy

2 Department of Applied Sciences, University "Parthenope" of Naples, Centro Direzionale Isola C4, Naples, 80143, Italy

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BMC Bioinformatics 2012, 13(Suppl 4):S19  doi:10.1186/1471-2105-13-S4-S19

Published: 28 March 2012

Abstract

Background

The development of accurate protein-protein docking programs is making this kind of simulations an effective tool to predict the 3D structure and the surface of interaction between the molecular partners in macromolecular complexes. However, correctly scoring multiple docking solutions is still an open problem. As a consequence, the accurate and tedious screening of many docking models is usually required in the analysis step.

Methods

All the programs under CONS-COCOMAPS have been written in python, taking advantage of python libraries such as SciPy and Matplotlib. CONS-COCOMAPS is freely available as a web tool at the URL:

http://www.molnac.unisa.it/BioTools/conscocomaps/ webcite.

Results

Here we presented CONS-COCOMAPS, a novel tool to easily measure and visualize the consensus in multiple docking solutions. CONS-COCOMAPS uses the conservation of inter-residue contacts as an estimate of the similarity between different docking solutions. To visualize the conservation, CONS-COCOMAPS uses intermolecular contact maps.

Conclusions

The application of CONS-COCOMAPS to test-cases taken from recent CAPRI rounds has shown that it is very efficient in highlighting even a very weak consensus that often is biologically meaningful.