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