iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines
Nicolas Renaud,
Yong Jung,
Vasant Honavar,
Cunliang Geng,
Alexandre M.J.J. Bonvin,
Li C. Xue
Affiliations
Nicolas Renaud
Netherlands eScience Center, Science Park 140, 1098 XG, Amsterdam, The Netherlands; Corresponding author.
Yong Jung
Bioinformatics & Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA
Vasant Honavar
Bioinformatics & Genomics Graduate Program, Pennsylvania State University, University Park, PA 16802, USA; College of Information Science & Technology, Pennsylvania State University, University Park, PA 16802, USA
Cunliang Geng
Netherlands eScience Center, Science Park 140, 1098 XG, Amsterdam, The Netherlands; Bijvoet Centre for Biomolecular Research Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Alexandre M.J.J. Bonvin
Bijvoet Centre for Biomolecular Research Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
Li C. Xue
Bijvoet Centre for Biomolecular Research Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Center for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
Computational docking is a promising tool to model three-dimensional (3D) structures of protein–protein complexes, which provides fundamental insights of protein functions in the cellular life. Singling out near-native models from the huge pool of generated docking models (referred to as the scoring problem) remains as a major challenge in computational docking. We recently published iScore, a novel graph kernel based scoring function. iScore ranks docking models based on their interface graph similarities to the training interface graph set. iScore uses a support vector machine approach with random-walk graph kernels to classify and rank protein–protein interfaces. Here, we present the software for iScore. The software provides executable scripts that fully automate the computational workflow. In addition, the creation and analysis of the interface graph can be distributed across different processes using Message Passing interface (MPI) and can be offloaded to GPUs thanks to dedicated CUDA kernels.
