ArticleNucleic acids research2015
The SUPERFAMILY 1.75 database in 2014: a doubling of data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed.
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- The dcGO Domain-Centric Ontology Database in 2023: New Website and Extended Annotations for Protein Structural Domains.Journal of molecular biology · 2023Article
- Improved global protein homolog detection with major gains in function identification.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
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- DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction.Bioinformatics (Oxford, England) · 2021Article
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- Abundance Imparts Evolutionary Constraints of Similar Magnitude on the Buried, Surface, and Disordered Regions of Proteins.Frontiers in molecular biosciences · 2021Article
- Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins.Frontiers in microbiology · 2021Article
- Classification and Computational Analysis ofFrontiers in genetics · 2020Article
- DISPOT: a simple knowledge-based protein domain interaction statistical potential.Bioinformatics (Oxford, England) · 2019Article
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10 authors.
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Abstract
We present updates to the SUPERFAMILY 1.75 (http://supfam.org) online resource and protein sequence collection. The hidden Markov model library that provides sequence homology to SCOP structural domains remains unchanged at version 1.75. In the last 4 years SUPERFAMILY has more than doubled its holding of curated complete proteomes over all cellular life, from 1400 proteomes reported previously in 2010 up to 3258 at present. Outside of the main sequence collection, SUPERFAMILY continues to provide domain annotation for sequences provided by other resources such as: UniProt, Ensembl, PDB, much of JGI Phytozome and selected subcollections of NCBI RefSeq. Despite this growth in data volume, SUPERFAMILY now provides users with an expanded and daily updated phylogenetic tree of life (sTOL). This tree is built with genomic-scale domain annotation data as before, but constantly updated when new species are introduced to the sequence library. Our Gene Ontology and other functional and phenotypic annotations previously reported have stood up to critical assessment by the function prediction community. We have now introduced these data in an integrated manner online at the level of an individual sequence, and--in the case of whole genomes--with enrichment analysis against a taxonomically defined background.
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