Annotation and Function

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

Found 55 links

Displaying 15 links

3D-FunTool Content

http://3dfun.bioinfo.pl

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.

ANNIETool Content

http://annie.bii.a-star.edu.sg

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.

BAR-PLUSTool Content

http://bar.biocomp.unibo.it/bar2.0

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.

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DBAliDatabase Content

http://salilab.org/DBAli/

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

ET Report MakerTool Content

http://mammoth.bcm.tmc.edu/report_maker/

Evolutionary trace (ET) report maker pools information from different sources including databases and on-the-fly multiple sequence analysis to produce a pdf formatted document as output. The emphasis is on prediction of functional sites of proteins.

FFPredTool Content

http://bioinf.cs.ucl.ac.uk/ffpred/

Using a machine learning approach, FFPred server predicts protein function using protein features scanned against a library of over 300 Gene Ontology annotation terms. FFPred has the capacity to annotate distant homologues and orphan protein sequences.

GCViewTool Content

http://toolkit.tuebingen.mpg.de/gcview

GCView facilitates the analysis of the genomic context of a query protein. It uses protein homology to assign corresponding genomic context.

This content is being maintained by dirk.linke and AG Linke.

Gene3DTool Content

http://gene3d.biochem.ucl.ac.uk/WebServices/

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.

This content is being maintained by corinyeats.

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GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

GObletTool Content

http://goblet.molgen.mpg.de/

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

GPCRpredTool Content

http://www.imtech.res.in/raghava/gpcrpred/

GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.

This content is being maintained by raghavagps.

Tags associated with subcategory 'Protein/Annotation and Function'

protein sequence analysis proteins humans protein databases algorithms computational biology animals molecular models sequence alignment protein conformation amino acid sequence homology systems integration reproducibility of results amino acid sequence genomics binding sites quaternary protein structure recombinant proteins ovomucin plant lectins plant proteins protein structural homology proprotein convertases chemical models structure-activity relationship enzymes computer simulation energy metabolism protein interaction mapping gene expression regulation succinate dehydrogenase saccharomyces cerevisiae online systems x-ray crystallography cytochrome p-450 enzyme system false positive reactions protein binding fungal proteins hydrogen bonding molecular structure entropy pharmaceutical preparations statistical data interpretation ligands heterotrimeric gtp-binding proteins drug design single nucleotide polymorphism muramidase missense mutation mutation phenotype repressor proteins pseudogenes markov chains biogenic amine receptors hiv integrase fabaceae signal transduction lectins molecular cloning medicinal plants enzyme inhibitors color dipeptides cholinergic receptors dopamine receptors serotonin receptors chymotrypsin beetles terminology as topic genes histones initiator codon leghemoglobin open reading frames molecular sequence data genome gene expression phylogeny molecular evolution software design tertiary protein structure factual databases tissue distribution peptides probability rna sequence analysis viral genome genetic databases sequence analysis nucleic acids messenger rna dna sequence analysis secondary protein structure proteome ubiquitin automation conserved sequence codon escherichia coli proteins chromosome mapping