ArticleBMC bioinformatics2010
A comparative study of conservation and variation scores.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Evolutionary conservation of sequence motifs at sites of protein modification.The Journal of biological chemistry · 2023Article
- Article
- Recent changes in the mutational dynamics of the SARS-CoV-2 main protease substantiate the danger of emerging resistance to antiviral drugs.Frontiers in medicine · 2022Article
- Article
- Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein.PLoS computational biology · 2020Article
- BALCONY: an R package for MSA and functional compartments of protein variability analysis.BMC bioinformatics · 2018Article
- PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction.Scientific reports · 2018Article
- Global computational mutagenesis provides a critical stability framework in protein structures.PloS one · 2017Article
- Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.International journal of molecular sciences · 2016Article
- ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.Nucleic acids research · 2016Article
- Causes of evolutionary rate variation among protein sites.Nature reviews. Genetics · 2016Review
- Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease 'driver' mutations.Scientific reports · 2015Article
- Sequence Conservation, Radial Distance and Packing Density in Spherical Viral Capsids.PloS one · 2015Article
- A creature with a hundred waggly tails: intrinsically disordered proteins in the ribosome.Cellular and molecular life sciences : CMLS · 2014Article
- Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals.BMC genomics · 2014Article
- Local packing density is the main structural determinant of the rate of protein sequence evolution at site level.BioMed research international · 2014Article
- Article
- Intrinsic disorder in the BK channel and its interactome.PloS one · 2014Article
- Protein structure based prediction of catalytic residues.BMC bioinformatics · 2013Article
- Bioinformatics analysis reveals biophysical and evolutionary insights into the 3-nitrotyrosine post-translational modification in the human proteome.Open biology · 2013Article
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2 authors.
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Abstract
backgroundConservation and variation scores are used when evaluating sites in a multiple sequence alignment, in order to identify residues critical for structure or function. A variety of scores are available today but it is not clear how different scores relate to each other.
resultsWe applied 25 conservation and variation scores to alignments from the Catalytic Site Atlas (CSA). We calculated distances among scores based on correlation coefficients, and constructed a dendrogram of the scores by average linking cluster analysis. The cluster analysis showed that most scores fall into one of two groups--substitution matrix based group and frequency based group respectively. We also evaluated the scores' performance in predicting catalytic sites and found that frequency based scores generally perform best.
conclusionsConservation and variation scores can be classified into mainly two large groups. When using a score to predict catalytic sites, frequency based scores that also consider a background distribution are most successful.
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