DockAnalyse : an application for the analysis of protein-protein interactions
Amela Abellan, Isaac (Universitat Autònoma de Barcelona. Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí")
Delicado, Pedro (Universitat Politècnica de Catalunya. Departament d'Estadística i Investigació Operativa)
Gómez Moruno, Antonio (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Bonàs, Sílvia (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Querol Murillo, Enrique (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Cedano Rodríguez, Juan Antonio (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)

Date:	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.
Grants:	Ministerio de Educación y Ciencia BIO2007-67904-C02-01 Ministerio de Ciencia e Innovación MTM2009-13985-C02-01 Ministerio de Ciencia e Innovación MTM2010-14887
Rights:	Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.
Language:	Anglès
Document:	Article ; recerca ; Versió publicada
Published in:	BMC Structural biology, Vol. 10, N. 37 (October 2010) , p., ISSN 1472-6807

DOI: 10.1186/1472-6807-10-37
PMID: 20969768

11 p, 1.8 MB

3.3 MB

The record appears in these collections:
Research literature > UAB research groups literature > Research Centres and Groups (research output) > Health sciences and biosciences > Institut de Biotecnologia i de Biomedicina (IBB)
Articles > Research articles
Articles > Published articles