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PMD specifications

Information


Unique identifier OMICS_22417
Name PMD
Alternative name Protein Mutant Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

Publication for Protein Mutant Database

PMD citations

 (8)
library_books

Computational predictors fail to identify amino acid substitution effects at rheostat positions

2017
Sci Rep
PMCID: 5278360
PMID: 28134345
DOI: 10.1038/srep41329

[…] 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 […]

library_books

Prediction of distal residue participation in enzyme catalysis

2015
PMCID: 4420525
PMID: 25627867
DOI: 10.1002/pro.2648

[…] 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/). […]

library_books

Prediction of the Damage Associated Non Synonymous Single Nucleotide Polymorphisms in the Human MC1R Gene

2015
PLoS One
PMCID: 4368538
PMID: 25794181
DOI: 10.1371/journal.pone.0121812

[…] 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 […]

library_books

Human Thromboxane A2 Receptor Genetic Variants: In Silico, In Vitro and “In Platelet” Analysis

2013
PLoS One
PMCID: 3696120
PMID: 23840660
DOI: 10.1371/journal.pone.0067314

[…] 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 […]

library_books

Algorithms and semantic infrastructure for mutation impact extraction and grounding

2010
BMC Genomics
PMCID: 3005927
PMID: 21143808
DOI: 10.1186/1471-2164-11-S4-S24

[…] 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 […]

library_books

Bi Directional SIFT Predicts a Subset of Activating Mutations

2009
PLoS One
PMCID: 2788704
PMID: 20011534
DOI: 10.1371/journal.pone.0008311

[…] 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 […]

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PMD institution(s)
Center for Information Biology, National Institute of Genetics, Shizuoka, Japan
PMD funding source(s)
Supported by a grant-in-aid from the Ministry of Education, Science, Sports and Culture, Japan.

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