The Protein Mutant Database

Abstract

Currently the protein mutant database (PMD) contains over 81 000 mutants, including artificial as well as natural mutants of various proteins extracted from about 10 000 articles. We recently developed a powerful viewing and retrieving system (http://pmd.ddbj.nig.ac.jp), which is integrated with the sequence and tertiary structure databases. The system has the following features: (i) mutated sequences are displayed after being automatically generated from the information described in the entry together with the sequence data of wild-type proteins integrated. This is a convenient feature because it allows one to see the position of altered amino acids (shown in a different color) in the entire sequence of a wild-type protein; (ii) for those proteins whose 3D structures have been experimentally determined, a 3D structure is displayed to show mutation sites in a different color; (iii) a sequence homology search against PMD can be carried out with any query sequence; (iv) a summary of mutations of homologous sequences can be displayed, which shows all the mutations at a certain site of a protein, recorded throughout the PMD.

A Family of Evolution–Entropy Hybrid Methods for Ranking Protein Residues by Importance

“…21,32 Specifically, we used entries containing reference to single-point mutations in proteins at least 70% identical with our test cases, annotated as either causing a complete loss of protein …”

“…As an alternative, we construct by literature search a tentative key residue set for several well-investigated proteins, a task in which we are greatly assisted by Protein Mutant Database. 21 We then estimate the quality of a method by its capability to rank the members of the key set highly. In other words, taking this set as a "gold standard", we study the sensitivityspecificity performance of a method.…”

Neutral and weakly nonneutral sequence variants may define individuality

“…Nonsynonymous single-nucleotide polymorphisms (nsSNPs) (here, nonsynonymous single-nucleotide variants of any population frequency), variants that alter the amino acid sequence, have been associated with many diseases (3). Because experimental findings are rarely reported to databases in a standardized form, metaresources, such as the Protein Mutant Database (PMD) (4) and Swiss-Prot/UniProt (5), manually curate publications to map variants to diseases. Natural language processing automates this mapping (6).…”

In Silico Functional Assessment of Sequence Variations: Predicting Phenotypic Functions of Novel Variations

“…Screening for Non-Acceptable Polymorphisms (SNAP) predicts non-neutral substitutions by using annotations from the protein mutant database (Kawabata et al, 1999) and by combining many sequence analysis tools in neural networks (NNs) (Bromberg et al, 2007;Bromberg et al, 2008a;Bromberg et al, 2008b). It also uses solvent accessibility, secondary structure, flexibility, SIFT results, and conservation information.…”