ArticleNucleic acids research2015
CATH FunFHMMer web server: protein functional annotations using functional family assignments.
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 29 papers.
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Who cites it
29 citing papers in PubMed.
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- ASMC: investigating the amino acid diversity of enzyme active sites.Bioinformatics (Oxford, England) · 2025Article
- Proteome-wide determinants of co-translational chaperone binding in bacteria.Nature communications · 2025Article
- Clustering protein functional families at large scale with hierarchical approaches.Protein science : a publication of the Protein Society · 2024Article
- Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics.Scientific reports · 2024Article
- Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies.Nature communications · 2023Article
- TEMPROT: protein function annotation using transformers embeddings and homology search.BMC bioinformatics · 2023Article
- Article
- Contrastive learning on protein embeddings enlightens midnight zone.NAR genomics and bioinformatics · 2022Article
- Assigning protein function from domain-function associations using DomFun.BMC bioinformatics · 2022Article
- Three-dimensional Structure Databases of Biological Macromolecules.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Clustering FunFams using sequence embeddings improves EC purity.Bioinformatics (Oxford, England) · 2021Article
- Role of Position K+4 in the Phosphorylation and Dephosphorylation Reaction Kinetics of the CheY Response Regulator.Biochemistry · 2021Article
- Heterologous expression of cyanobacterialPlant biotechnology reports · 2021Article
- GODoc: high-throughput protein function prediction using novel k-nearest-neighbor and voting algorithms.BMC bioinformatics · 2020Article
- EnzyMine: a comprehensive database for enzyme function annotation with enzymatic reaction chemical feature.Database : the journal of biological databases and curation · 2020Article
- Genomic Signature of Shifts in Selection in a Subalpine Ant and Its Physiological Adaptations.Molecular biology and evolution · 2020Article
- NetGO: improving large-scale protein function prediction with massive network information.Nucleic acids research · 2019Article
- A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations.Scientific reports · 2019Article
- PANNZER2: a rapid functional annotation web server.Nucleic acids research · 2018Article
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Authors and funding
7 authors.
Funding
Abstract
The widening function annotation gap in protein databases and the increasing number and diversity of the proteins being sequenced presents new challenges to protein function prediction methods. Multidomain proteins complicate the protein sequence-structure-function relationship further as new combinations of domains can expand the functional repertoire, creating new proteins and functions. Here, we present the FunFHMMer web server, which provides Gene Ontology (GO) annotations for query protein sequences based on the functional classification of the domain-based CATH-Gene3D resource. Our server also provides valuable information for the prediction of functional sites. The predictive power of FunFHMMer has been validated on a set of 95 proteins where FunFHMMer performs better than BLAST, Pfam and CDD. Recent validation by an independent international competition ranks FunFHMMer as one of the top function prediction methods in predicting GO annotations for both the Biological Process and Molecular Function Ontology. The FunFHMMer web server is available at http://www.cathdb.info/search/by_funfhmmer.
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