ArticleProteins2004
Analysis of protein homology by assessing the (dis)similarity in protein loop regions.
Article in Proteins, 2004. 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.
- Generation of a Soluble African Horse Sickness Virus VP7 Protein Capable of Forming Core-like Particles.Viruses · 2022Article
- An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.PLoS biology · 2016Article
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Characteristics of Epstein-Barr virus envelope protein gp42.Virus genes · 2010Article
- Functional states of homooligomers: insights from the evolution of glycosyltransferases.Journal of molecular biology · 2010Article
- Mining protein loops using a structural alphabet and statistical exceptionality.BMC bioinformatics · 2010Article
- Analysis of loop boundaries using different local structure assignment methods.Protein science : a publication of the Protein Society · 2009Article
- Coevolution in defining the functional specificity.Proteins · 2009Article
- Ribonuclease A homologues of the zebrafish: polymorphism, crystal structures of two representatives and their evolutionary implications.Journal of molecular biology · 2008Article
- Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets.Journal of molecular biology · 2008Article
- Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions.BMC bioinformatics · 2007Article
- Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins.BMC structural biology · 2007Article
- New metrics for comparative genomics.Current opinion in biotechnology · 2006Review
- Evolutionary plasticity of protein families: coupling between sequence and structure variation.Proteins · 2005Article
- Structural similarity of loops in protein families: toward the understanding of protein evolution.BMC evolutionary biology · 2005Article
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Authors and funding
2 authors.
Funding
Abstract
Two proteins are considered to have a similar fold if sufficiently many of their secondary structure elements are positioned similarly in space and are connected in the same order. Such a common structural scaffold may arise due to either divergent or convergent evolution. The intervening unaligned regions ("loops") between the superimposable helices and strands can exhibit a wide range of similarity and may offer clues to the structural evolution of folds. One might argue that more closely related proteins differ less in their nonconserved loop regions than distantly related proteins and, at the same time, the degree of variability in the loop regions in structurally similar but unrelated proteins is higher than in homologs. Here we introduce a new measure for structural (dis)similarity in loop regions that is based on the concept of the Hausdorff metric. This measure is used to gauge protein relatedness and is tested on a benchmark of homologous and analogous protein structures. It has been shown that the new measure can distinguish homologous from analogous proteins with the same or higher accuracy than the conventional measures that are based on comparing proteins in structurally aligned regions. We argue that this result can be attributed to the higher sensitivity of the Hausdorff (dis)similarity measure in detecting particularly evident dissimilarities in structures and draw some conclusions about evolutionary relatedness of proteins in the most populated protein folds.
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