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Open Access Highly Accessed Methodology article

DockAnalyse: an application for the analysis of protein-protein interactions

Isaac Amela1, Pedro Delicado2, Antonio Gómez1, Sílvia Bonàs1, Enrique Querol1 and Juan Cedano1*

Author Affiliations

1 Institut de Biotecnologia i de Biomedicina Parc de Recerca UAB and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona. 08193-Bellaterra, Barcelona, Spain

2 Departament d'Estadística i Investigació Operativa, Universitat Politècnica de Catalunya. 08034-Barcelona, Spain

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BMC Structural Biology 2010, 10:37  doi:10.1186/1472-6807-10-37

Published: 22 October 2010

Abstract

Background

Is it possible to identify what the best solution of a docking program is? The usual answer to this question is the highest score solution, but interactions between proteins are dynamic processes, and many times the interaction regions are wide enough to permit protein-protein interactions with different orientations and/or interaction energies. In some cases, as in a multimeric protein complex, several interaction regions are possible among the monomers. These dynamic processes involve interactions with surface displacements between the proteins to finally achieve the functional configuration of the protein complex. Consequently, there is not a static and single solution for the interaction between proteins, but there are several important configurations that also have to be analyzed.

Results

To extract those representative solutions from the docking output datafile, we have developed an unsupervised and automatic clustering application, named DockAnalyse. This application is based on the already existing DBscan clustering method, which searches for continuities among the clusters generated by the docking output data representation. The DBscan clustering method is very robust and, moreover, solves some of the inconsistency problems of the classical clustering methods like, for example, the treatment of outliers and the dependence of the previously defined number of clusters.

Conclusions

DockAnalyse makes the interpretation of the docking solutions through graphical and visual representations easier by guiding the user to find the representative solutions. We have applied our new approach to analyze several protein interactions and model the dynamic protein interaction behavior of a protein complex. DockAnalyse might also be used to describe interaction regions between proteins and, therefore, guide future flexible dockings. The application (implemented in the R package) is accessible.