Protein Mutant Database

[…] variant-effect prediction tools not selected for the PredictSNP pipeline: SNPs&GO, MutPred, PON-P and HumVar; the fifth source is a subset of UniProt variants). Testing datasets are derived from the Protein Mutant Database (PMD) and from experimental studies.Meta-SNP is a random forest-based binary classifier meta-predictor, combining the predictions of four methods (SNAP2, SIFT, PANTHER, PhD-SNP […]

[…] e considered first-shell for this study.Experimental mutagenesis data reported previously were obtained from individual literature references, with the help of the BRENDA enzyme database and from the Protein Mutant Database (http://www.genome.ad.jp/dbget-bin/www_bfind?pmd) within the DBGET database retrieval system (http://www.genome.jp/dbget/). […]

[…] e scores are transformed to percentages to allow comparison, and the individual predictions are combined in the consensus prediction. The predictions are supplemented by experimental annotations from Protein Mutant Database and Uniprot [].In order to identify the nsSNPs more probably damaging in the gene the categorical prediction of the individual tools were combined by the count of damage result […]

[…] PSI-BLAST alignment conservation, while incorporating additional sequence information including solvent accessibility and secondary structure (PROF), flexibility (PROFbval), and annotations from PMD (Protein Mutant Database) and. As with SIFT, SNAP reports a tolerance range from 0 (damaging) to 1 (neutral). PolyPhen (PPH) (http://genetics.bwh.harvard.edu/pph/) has been superseded by PolyPhen-2 (P […]

[…] es is crucial to the understanding of genetic mechanisms, biological processes and the complex diseases or phenotypes that may result. Despite attempts to manually organize variation information e.g. Protein Mutant Database [] and Human Genome Variation Society [], the amount of information is increasing exponentially so that such databases are perpetually out of date, and having a latency of many […]

[…] ify at least a subset of activating mutations that would not otherwise be identified by SIFT.We further attempted to validate B-SIFT's ability to identify activating mutations through analysis of the Protein Mutant Database (PMD), a database of literature-curated protein mutants and phenotypes . Although PMD contained a large number of mutations with phenotype descriptions and annotations, the int […]