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Bioinformatics. 2016 Mar 15;32(6):940-2. doi: 10.1093/bioinformatics/btv666. Epub 2015 Nov 14.

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

Author information

1
Department of Chemistry and Biochemistry, UC, San Diego, La Jolla, CA 92093-0359 USA.

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.

PMID:
26568623
PMCID:
PMC4907390
DOI:
10.1093/bioinformatics/btv666
[Indexed for MEDLINE]
Free PMC Article

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