ArticleNucleic acids research2009
HorA web server to infer homology between proteins using sequence and structural similarity.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains.Neuron · 2016Article
- Article
- Manual classification strategies in the ECOD database.Proteins · 2015Article
- ECOD: an evolutionary classification of protein domains.PLoS computational biology · 2014Article
- Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.Protein science : a publication of the Protein Society · 2014Article
- iPBA: a tool for protein structure comparison using sequence alignment strategies.Nucleic acids research · 2011Article
- CASP9 target classification.Proteins · 2011Article
- Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity.The Journal of biological chemistry · 2010Article
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Authors and funding
3 authors.
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Abstract
The biological properties of proteins are often gleaned through comparative analysis of evolutionary relatives. Although protein structure similarity search methods detect more distant homologs than purely sequence-based methods, structural resemblance can result from either homology (common ancestry) or analogy (similarity without common ancestry). While many existing web servers detect structural neighbors, they do not explicitly address the question of homology versus analogy. Here, we present a web server named HorA (Homology or Analogy) that identifies likely homologs for a query protein structure. Unlike other servers, HorA combines sequence information from state-of-the-art profile methods with structure information from spatial similarity measures using an advanced computational technique. HorA aims to identify biologically meaningful connections rather than purely 3D-geometric similarities. The HorA method finds approximately 90% of remote homologs defined in the manually curated database SCOP. HorA will be especially useful for finding remote homologs that might be overlooked by other sequence or structural similarity search servers. The HorA server is available at http://prodata.swmed.edu/horaserver.
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