ArticleJournal of molecular biology2008
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- Assessing Structural Classification Using AlphaFold2 Models Through ECOD-Based Comparative Analysis.Proteins · 2025Article
- Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction.Journal of molecular biology · 2021Review
- Bridging Themes: Short Protein Segments Found in Different Architectures.Molecular biology and evolution · 2021Article
- 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
- MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C(α) only models, Alternative alignments, and Non-sequential alignments.BMC bioinformatics · 2013Article
- Defining and predicting structurally conserved regions in protein superfamilies.Bioinformatics (Oxford, England) · 2013Article
- Protein structure alignment beyond spatial proximity.Scientific reports · 2013Article
- On universal common ancestry, sequence similarity, and phylogenetic structure: the sins of P-values and the virtues of Bayesian evidence.Biology direct · 2011Article
- Protein structure determination by exhaustive search of Protein Data Bank derived databases.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison.BMC bioinformatics · 2010Article
- HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.Bioinformatics (Oxford, England) · 2009Article
- Exploration of uncharted regions of the protein universe.PLoS biology · 2009Article
- COMPASS server for homology detection: improved statistical accuracy, speed and functionality.Nucleic acids research · 2009Article
- HorA web server to infer homology between proteins using sequence and structural similarity.Nucleic acids research · 2009Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
A natural way to study protein sequence, structure, and function is to put them in the context of evolution. Homologs inherit similarities from their common ancestor, while analogs converge to similar structures due to a limited number of energetically favorable ways to pack secondary structural elements. Using novel strategies, we previously assembled two reliable databases of homologs and analogs. In this study, we compare these two data sets and develop a support vector machine (SVM)-based classifier to discriminate between homologs and analogs. The classifier uses a number of well-known similarity scores. We observe that although both structure scores and sequence scores contribute to SVM performance, profile sequence scores computed based on structural alignments are the best discriminators between remote homologs and structural analogs. We apply our classifier to a representative set from the expert-constructed database, Structural Classification of Proteins (SCOP). The SVM classifier recovers 76% of the remote homologs defined as domains in the same SCOP superfamily but from different families. More importantly, we also detect and discuss interesting homologous relationships between SCOP domains from different superfamilies, folds, and even classes.
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