ArticleNucleic acids research2016
PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- PASS2: update of database of structure-based sequence alignments.Database : the journal of biological databases and curation · 2025Article
- PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.Database : the journal of biological databases and curation · 2019Article
- GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies.Database : the journal of biological databases and curation · 2019Article
- RStrucFam: a web server to associate structure and cognate RNA for RNA-binding proteins from sequence information.BMC bioinformatics · 2016Article
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5 authors.
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Abstract
Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/.
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