ArticleBMC bioinformatics2009
Ensemble approach to predict specificity determinants: benchmarking and validation.
Article in BMC bioinformatics, 2009. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
15 citing papers in PubMed.
- Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity.Bioengineering (Basel, Switzerland) · 2021Article
- Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.Scientific reports · 2020Article
- Article
- Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.PLoS computational biology · 2016Article
- SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments.Nucleic acids research · 2013Article
- Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction.BMC bioinformatics · 2012Article
- SPEER-SERVER: a web server for prediction of protein specificity determining sites.Nucleic acids research · 2012Article
- Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures.BMC bioinformatics · 2012Article
- Cube-DB: detection of functional divergence in human protein families.Nucleic acids research · 2012Article
- Surveying the manifold divergence of an entire protein class for statistical clues to underlying biochemical mechanisms.Statistical applications in genetics and molecular biology · 2011Article
- Determinants, discriminants, conserved residues--a heuristic approach to detection of functional divergence in protein families.PloS one · 2011Article
- Bayesian classification of residues associated with protein functional divergence: Arf and Arf-like GTPases.Biology direct · 2010Article
- Multi-Harmony: detecting functional specificity from sequence alignment.Nucleic acids research · 2010Article
- Visualization of multiple alignments, phylogenies and gene family evolution.Nature methods · 2010Review
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundIt is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking protocol was employed to provide a reliable evaluation of methods which predict the specificity determining sites. Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results.
resultsIt was shown that the analysis of structural characteristics of predicted specificity determining sites might provide the means to validate their prediction accuracy. For example, we found that for smaller distances it holds true that the more reliable the prediction method is, the closer predicted specificity determining sites are to each other and to the ligand.
conclusionWe observed certain similarities of structural features between predicted and actual subsites which might point to their functional relevance. We speculate that majority of the identified potential specificity determining sites might be indirectly involved in specific interactions and could be ideal target for mutagenesis experiments.
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