ArticleBMC structural biology2009
Improving protein structure similarity searches using domain boundaries based on conserved sequence information.
Article in BMC structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Unusual traits shape the architecture of the Ig ancestor molecule.Communications biology · 2025Article
- UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions.Nucleic acids research · 2013Article
- Structure- and sequence-based function prediction for non-homologous proteins.Journal of structural and functional genomics · 2012Article
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4 authors.
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Abstract
backgroundThe identification of protein domains plays an important role in protein structure comparison. Domain query size and composition are critical to structure similarity search algorithms such as the Vector Alignment Search Tool (VAST), the method employed for computing related protein structures in NCBI Entrez system. Currently, domains identified on the basis of structural compactness are used for VAST computations. In this study, we have investigated how alternative definitions of domains derived from conserved sequence alignments in the Conserved Domain Database (CDD) would affect the domain comparisons and structure similarity search performance of VAST.
resultsAlternative domains, which have significantly different secondary structure composition from those based on structurally compact units, were identified based on the alignment footprints of curated protein sequence domain families. Our analysis indicates that domain boundaries disagree on roughly 8% of protein chains in the medium redundancy subset of the Molecular Modeling Database (MMDB). These conflicting sequence based domain boundaries perform slightly better than structure domains in structure similarity searches, and there are interesting cases when structure similarity search performance is markedly improved.
conclusionStructure similarity searches using domain boundaries based on conserved sequence information can provide an additional method for investigators to identify interesting similarities between proteins with known structures. Because of the improvement in performance of structure similarity searches using sequence domain boundaries, we are in the process of implementing their inclusion into the VAST search and MMDB resources in the NCBI Entrez system.
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