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Advances in Bioinformatics
Volume 2014, Article ID 278385, 7 pages
http://dx.doi.org/10.1155/2014/278385
Research Article

AUTO-MUTE 2.0: A Portable Framework with Enhanced Capabilities for Predicting Protein Functional Consequences upon Mutation

Laboratory for Structural Bioinformatics, School of Systems Biology, George Mason University, Manassas, VA 20110, USA

Received 11 June 2014; Revised 29 July 2014; Accepted 29 July 2014; Published 17 August 2014

Academic Editor: Gilbert Deleage

Copyright © 2014 Majid Masso and Iosif I. Vaisman. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The AUTO-MUTE 2.0 stand-alone software package includes a collection of programs for predicting functional changes to proteins upon single residue substitutions, developed by combining structure-based features with trained statistical learning models. Three of the predictors evaluate changes to protein stability upon mutation, each complementing a distinct experimental approach. Two additional classifiers are available, one for predicting activity changes due to residue replacements and the other for determining the disease potential of mutations associated with nonsynonymous single nucleotide polymorphisms (nsSNPs) in human proteins. These five command-line driven tools, as well as all the supporting programs, complement those that run our AUTO-MUTE web-based server. Nevertheless, all the codes have been rewritten and substantially altered for the new portable software, and they incorporate several new features based on user feedback. Included among these upgrades is the ability to perform three highly requested tasks: to run “big data” batch jobs; to generate predictions using modified protein data bank (PDB) structures, and unpublished personal models prepared using standard PDB file formatting; and to utilize NMR structure files that contain multiple models.