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Termini-Oriented Protein Function INferred Database
Abbreviation:TopFIND
General Information
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.
How to cite this record
FAIRsharing.org: TopFIND; Termini-Oriented Protein Function INferred Database; DOI: https://doi.org/10.25504/FAIRsharing.rkpmhn;
Last edited: Jan. 8, 2019, 1:15 p.m.; Last accessed: Jun 03 2020 10:45 p.m.
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Edits to 'https://fairsharing.org/FAIRsharing.rkpmhn' by 'The FAIRsharing Team' at 10:07, 21 Nov 2018 (approved):
'domains' has been modified:
Before:
Alternative splicing
Annotation
C-terminal amino acid residue
Evidence
Life Science
Molecular interaction
N-terminal amino acid residue
Network model
Protease cleavage
Protease site
Protein C-terminus binding
Protein N-terminus binding
Protein domain
Protein modification
Proteolytic digest
Protocol
Sequence annotation
Translation initiation
After:
Alternative splicing
Amino acid sequence
Annotation
C-terminal amino acid residue
Evidence
Life Science
Molecular interaction
N-terminal amino acid residue
Network model
Protease cleavage
Protease site
Protein C-terminus binding
Protein N-terminus binding
Protein domain
Protein modification
Proteolytic digest
Protocol
Sequence annotation
Translation initiation
Added:
Amino acid sequence
Removed:
Access / Retrieve Data
Conditions of Use
Data Versioning
| no versioning
|
No link recorded |
| access to historical database dumps possible
|
No link recorded |
Data Release
| ad-hoc release
|
No link recorded |
Data Curation
| automated curation
|
No link recorded |
| manual curation
|
No link recorded |
Data Access
Other Web Services
Publications
Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events
Nikolaus Fortelny, Sharon Yang, Paul Pavlidis, Philipp F Lange, Christopher M Overall
Nucleic Acids Research 2014
View Paper (PubMed)
View Publication
TopFIND 2.0—linking protein termini with proteolytic processing and modifications altering protein function
Philipp F Lange, Pitter F Huesgen, Christopher M Overall
Nucleic Acids Research 2012
View Paper (PubMed)
View Publication
Related Standards
Reporting Guidelines
No guidelines defined
Identifier Schemas
No identifier schema standards defined
Metrics
No metrics standards defined
Related Databases
No related databases defined
Implementing Policies
This record is not implemented by any policy.
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