How to cite this record: FAIRsharing.org: PSI-MOD; Protein MODification; DOI: https://doi.org/10.25504/FAIRsharing.2m4ms9; Last edited: Feb. 22, 2018, 2:02 p.m.; Last accessed: Mar 20 2018 7:48 a.m.
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A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.
PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as well as providing structural and functional annotation and access to large-scale data sets.
Termini-Oriented Protein Function INferred Database
TopFIND is a protein-centric database for the annotation of protein termini currently in its third version. Non-canonical protein termini can be the result of multiple different biological processes, including pre-translational processes such as alternative splicing and alternative translation initiation or post-translational protein processing by proteases that cleave proteases as part of protein maturation or as a regulatory modification. Accordingly, protein termini evidence in TopFIND is inferred from other databases such as ENSEMBL transcripts, TISdb for alternative translation initiation, MEROPS for protein cleavage by proteases, and UniProt for canonical and protein isoform start sites. Additionally, termini are annotated from user submitted lists of termini and inferred from user submitted lists of cleavage sites. As a protein-centric database, TopFIND presents a website for each protein isoform (organized around UniProt accession codes). These websites contain general protein information, such as organism, chromosome location, and proteins sequence. They then list position information such as specific termini evidences, known cleavage sites, sequence features and domains for each protein. In addition, TopFIND shows each protein in the context of the protease web, a network of proteases and their inhibitors, where a protease can cleave of other proteases and their inhibitors thus influencing their activity. All information in TopFIND can be filtered by a powerful filter engine that relies on rich annotation as to the origin of data in TopFIND. TopFIND can also be programmatically queried using the PSICQUIC or XML API. Recently, software tools were developed to enable quick access to TopFIND data for lists of termini obtained by, for example, proteomic termini screens (terminomics). TopFIND Explorer “TopFINDer” reports position specific protein information for protein termini, such as terminus evidences, prime and non-prime sequences, and protein domains affected by cleavage. TopFINDer further reports summary statistics for protein cleavage by known proteases. PathFINDer is a second tool that reports proteolytic paths from a query protease to identified protein substrates thus enabling the differentiation between direct and indirect protease substrates and yielding mechanistic insights into pathways based on existing information.
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