Annotation and Function

This section contains links to tools for annotating proteins and predicting protein function, localization, and other classifications.

Found 81 links

Displaying 15 links

3D-FunTool Content

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3D-Fun is software for predicting enzyme function from structure rather than sequence. Users input protein coordinates in PDB format to which all known protein structures are compared by 3D structural superposition. Superposition results are displayed through interactive graphics.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
3D-Fun: predicting enzyme function from structure20086

ANNIETool Content

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ANNIE integrates over twenty protein function prediction tools in a single website. ANNIE displays prediction results in an integrated manner using an innovative AJAX-based sequence viewer.

links directory index: 15
TitlePublication YearGoogle Scholar Citation Count
ANNIE: integrated de novo protein sequence annotation200915

BAR-PLUSTool Content

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BAR-PLUS is a web tool for functional and structural annotation of protein sequences based on a large scale genome cross comparison and a non-hierarchical clustering procedure. Sequence annotation is derived from UniProtKB, GO, Pfam and PDB.

BeAtMuSiCTool Content

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BeAtMuSiC is a coarse-grained predictor of the changes in binding free energy induced by point mutations, using the structure of the protein-protein complex as input.

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BLANNOTATORTool Content

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Blannotator is a rapid tool for functional prediction of gene or proteins sequences. The tool accepts DNA or protein sequences, given in FASTA-format, and performs a Blast homology search against UniProtKB databases. Matching sequences with similar annotations are merged into families of similar descriptions, which are, in turn, further unified, based on assigned GO-profiles retrieved from GOA, into sets of functionally equivalent sequences. As a result, a reliable description will be obtained.

This content is being maintained by mkankain.

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BYKdbDatabase Content

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Bacterial protein tYrosine Kinase database (BYKdb). Bacterial tyrosine-kinases share no resemblance with their eukaryotic counterparts and they have been unified in a new protein family named BY-kinases. However, BY-kinase sequence annotations in primary databases remain incomplete. This prompted us to develop a specialized database of computer-annotated BY-kinase sequences.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BYKdb: the Bacterial protein tYrosine Kinase database20121

CharProtDBDatabase Content

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CharProtDB is a curated database of biochemically characterized proteins. The initial data set in CharProtDB was collected through manual literature curation, and has been expanded by importing selected records from publicly available protein collections. Annotations in CharProtDB include gene name, symbol and various controlled vocabulary terms, including Gene Ontology terms, Enzyme Commission number and TransportDB accession.

COFACTORTool Content

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COFACTOR is a structure based method for annotating the biological function of proteins. Users input a 3D structure of their protein of interest and COFACTOR threads the structure through functional libraries to identify functional site homology. The COFACTOR algorithm ranked in the CASP9 experiments (2010) for function prediction.

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CombFuncTool Content

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CombFunc is an automated method for the Gene Ontology based prediction of protein function. Users can either submit a sequence or use a Uniprot identifier.

This content is being maintained by markwass.

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dbCANTool Content

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dbCAN provides automated carbohydrate-active enzyme signature domain-based annotation for a set of proteins. Each carbohydrate-active enzyme has an assigned signature domain.

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DETECTTool Content

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A density estimation tool for enzyme classification and its application to Plasmodium falciparum. DETECT, a probabilistic method for enzyme prediction that accounts for the sequence diversity across enzyme families. By comparing the global alignment scores of an unknown protein to those of all known enzymes, an integrated likelihood score can be readily calculated, ranking the reaction classes relevant for that protein.

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