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

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.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.Protein-protein interaction (PPI) is the key process by which most of the proteins fulfill their function, and interactomics represents one of the current frontiers of biosciences [1,2]. It is well known that many proteins are single parts, called monomers, of a complex quaternary structure, a multimer. In any case, monomers alone do not have a specific function which is only achieved when the distinct parts interact together to accomplish a certain function [3,4]. PPIs can help us to predict protein function and, therefore, many protein function predictors have been developed using PPI databases [5-11]. Due to PPIs, it is expected that in the near future the number of protein complexes will surpass the number of proteins in some organisms. A lot of PPIs involve surface displacements among the members of the protein complex to achieve the required biological function.Nuclear Magnetic Res