ArticleBioinformatics (Oxford, England)2012
Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- ProtCID: a data resource for structural information on protein interactions.Nature communications · 2020Article
- Atypical structural tendencies among low-complexity domains in the Protein Data Bank proteome.PLoS computational biology · 2020Article
- Genome-Wide Identification and Characterization of the Mitochondrial Transcription Termination Factors (mTERFs) inInternational journal of molecular sciences · 2019Article
- Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions.Nucleic acids research · 2019Article
- HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies.Genome biology · 2018Article
- Use of designed sequences in protein structure recognition.Biology direct · 2018Article
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2 authors.
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Abstract
motivationAutomating the assignment of existing domain and protein family classifications to new sets of sequences is an important task. Current methods often miss assignments because remote relationships fail to achieve statistical significance. Some assignments are not as long as the actual domain definitions because local alignment methods often cut alignments short. Long insertions in query sequences often erroneously result in two copies of the domain assigned to the query. Divergent repeat sequences in proteins are often missed.
resultsWe have developed a multilevel procedure to produce nearly complete assignments of protein families of an existing classification system to a large set of sequences. We apply this to the task of assigning Pfam domains to sequences and structures in the Protein Data Bank (PDB). We found that HHsearch alignments frequently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, leading to erroneous assignment at the Pfam family level. A greedy algorithm allowing for partial overlaps was, thus, applied first to sequence/HMM alignments, then HMM-HMM alignments and then structure alignments, taking care to join partial alignments split by large insertions into single-domain assignments. Additional assignment of repeat Pfams with weaker E-values was allowed after stronger assignments of the repeat HMM. Our database of assignments, presented in a database called PDBfam, contains Pfams for 99.4% of chains >50 residues. AVAILABILITY: The Pfam assignment data in PDBfam are available at http://dunbrack2.fccc.edu/ProtCid/PDBfam, which can be searched by PDB codes and Pfam identifiers. They will be updated regularly.
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