Gene3D -- comprehensive structural and functional annotation of genomes
What you can do:
Find structural and functional annotation of most available protein sequences.
Highlights:
- Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins.
- A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences.
- The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3.
- The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website.
- The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes.
- Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins.
- Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.
Keywords:
- sequence to structure analysis
- protein structures
- protein families
- protein domain assignments
- protein domains
- genome annotations
- proteome annotation
- protein sequence annotation
- protein function prediction
- protein evolution
- metabolic pathway
- protein-protein interaction
Literature & Tutorials:
PubMed Link: Gene3D -- Structural assignments for the biologist and bioinformaticist alike
-- 2006 Update: Gene3D: modelling protein structure, function and evolution
-- 2008 Update: Gene3D: comprehensive structural and functional annotation of genomes
-- -- 2010 Update: Gene3D: merging structure and function for a Thousand genomes
-- 2006 Update: Gene3D: modelling protein structure, function and evolution
-- 2008 Update: Gene3D: comprehensive structural and functional annotation of genomes
-- -- 2010 Update: Gene3D: merging structure and function for a Thousand genomes
This record last updated: 02-11-2010