ArticleNucleic acids research2007
STRALCP--structure alignment-based clustering of proteins.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Computational studies on rep and capsid proteins of CRESS DNA viruses.Virusdisease · 2024Article
- The core sequence of PIF competes for insulin/amyloid β in insulin degrading enzyme: potential treatment for Alzheimer's disease.Oncotarget · 2018Article
- Review
- Improved metrics for comparing structures of macromolecular assemblies determined by 3D electron-microscopy.Journal of structural biology · 2017Article
- Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm.mBio · 2016Article
- Automatic classification of protein structures relying on similarities between alignments.BMC bioinformatics · 2012Article
- Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types.BMC research notes · 2012Article
- CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms.Bioinformatics (Oxford, England) · 2011Article
- StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.BMC bioinformatics · 2011Article
- Cross-over between discrete and continuous protein structure space: insights into automatic classification and networks of protein structures.PLoS computational biology · 2009Article
- Touring protein space with Matt.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein structural annotation and classification is an important and challenging problem in bioinformatics. Research towards analysis of sequence-structure correspondences is critical for better understanding of a protein's structure, function, and its interaction with other molecules. Clustering of protein domains based on their structural similarities provides valuable information for protein classification schemes. In this article, we attempt to determine whether structure information alone is sufficient to adequately classify protein structures. We present an algorithm that identifies regions of structural similarity within a given set of protein structures, and uses those regions for clustering. In our approach, called STRALCP (STRucture ALignment-based Clustering of Proteins), we generate detailed information about global and local similarities between pairs of protein structures, identify fragments (spans) that are structurally conserved among proteins, and use these spans to group the structures accordingly. We also provide a web server at http://as2ts.llnl.gov/AS2TS/STRALCP/ for selecting protein structures, calculating structurally conserved regions and performing automated clustering.
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