iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

Abstract

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.

Keywords

• Protein–protein docking
• Scoring
• Graph kernel functions
• Support vector machines
• MPI
• Position-specific scoring matrix (PSSM)