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288
Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions
- Nucleic Acids Res
, 2013
"... Detection of protein homology via sequence similar-ity has important applications in biology, from protein structure and function prediction to recon-struction of phylogenies. Although current methods for aligning protein sequences are powerful, chal-lenges remain, including problems with homologous ..."
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Detection of protein homology via sequence similar-ity has important applications in biology, from protein structure and function prediction to recon-struction of phylogenies. Although current methods for aligning protein sequences are powerful, chal-lenges remain, including problems with homologous overextension of alignments and with regions under convergent evolution. Here, we test the ability of the profile hidden Markov model method HMMER3 to correctly assign homologous sequences to>13000 manually curated families from the Pfam database. We identify problem families using protein regions that match two or more Pfam families not currently annotated as related in Pfam. We find that HMMER3 E-value estimates seem to be less accurate for families that feature periodic patterns of compositional bias, such as the ones typically observed in coiled-coils. These results support the continued use of manually curated in-clusion thresholds in the Pfam database, especially on the subset of families that have been identified as problematic in experiments such as these. They also highlight the need for developing new methods that can correct for this particular type of compositional bias.
IMG 4 version of the integrated microbial genomes comparative analysis system
- Nucl. Acids Res
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TreeFam v9: a new website, more species and orthology-on-the-fly
- Nucleic Acids Res
, 2014
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Making your database available through Wikipedia: The Pros and Cons
- Nucleic Acids Res
, 2012
"... doi:10.1093/nar/gkr1195 ..."
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APPRIS: annotation of principal and alternative splice isoforms
- Nucleic Acids Res
, 2013
"... Here, we present APPRIS ..."
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Dfam: a database of repetitive DNA based on profile hidden Markov models
, 2012
"... We present a database of repetitive DNA elements, called Dfam ..."
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We present a database of repetitive DNA elements, called Dfam
Gene3D: multi-domain annotations for protein sequence and comparative genome analysis
- Nucleic Acids Res
, 2014
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SCOP2 prototype: a new approach to protein structure mining
- Nucleic Acids Res
, 2014
"... We present a prototype of a new structural classifi-cation of proteins, SCOP2 ..."
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Cited by 6 (2 self)
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We present a prototype of a new structural classifi-cation of proteins, SCOP2
doi:10.1093/nar/gkr998 PDBe: Protein Data Bank in Europe
, 2011
"... The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make struct ..."
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The Protein Data Bank in Europe (PDBe; pdbe.org) is a partner in the Worldwide PDB organization (wwPDB; wwpdb.org) and as such actively involved in managing the single global archive of biomacromolecular structure data, the PDB. In addition, PDBe develops tools, services and resources to make structure-related data more accessible to the biomedical community. Here we describe recently developed, extended or improved services, including an animated structure-presentation widget (PDBportfolio), a widget to graphically display the coverage of any UniProt sequence in the PDB (UniPDB), chemistry- and taxonomy-based PDB-archive browsers (PDBeXplore), and a tool for interactive visualization of NMR structures, corresponding experimental data as well as validation and analysis results (Vivaldi).
CombFunc: predicting protein function using heterogeneous data sources. Nucleic Acids Res. 2012;40(Web Server issue):W466–470
"... Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein s ..."
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Only a small fraction of known proteins have been functionally characterized, making protein function prediction essential to propose annotations for uncharacterized proteins. In recent years many function prediction methods have been developed using various sources of biological data from protein sequence and structure to gene expression data. Here we present the CombFunc web server, which makes Gene Ontology (GO)-based protein function predictions. CombFunc incorporates ConFunc, our existing function prediction method, with other approaches for function prediction that use protein sequence, gene expression and protein–protein interaction data. In benchmarking on a set of 1686 proteins CombFunc obtains preci-sion and recall of 0.71 and 0.64 respectively for gene ontology molecular function terms. For biological process GO terms precision of 0.74 and recall of 0.41 is obtained. CombFunc is available at
