MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction

Abstract

Motivation: MIEC-SVM is a structure-based method for predicting protein recognition specificity. Here, we present an automated MIEC-SVM pipeline providing an integrated and user-friendly workflow for construction and application of the MIEC-SVM models. This pipeline can handle standard amino acids and those with post-translational modifications (PTMs) or small molecules. Moreover, multi-threading and support to Sun Grid Engine (SGE) are implemented to significantly boost the computational efficiency.

Availability and implementation: The program is available at http://wanglab.ucsd.edu/MIEC-SVM CONTACT: : wei-wang@ucsd.edu

Supplementary information: Supplementary data available at Bioinformatics online.