ArticleAmino acids2008
Estimating residue evolutionary conservation by introducing von Neumann entropy and a novel gap-treating approach.
Article in Amino acids, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT06932601 (The Validity of a Novel Diabetes Diagnostic Device and Its Feasibility as Metabolic Syndrome Diagnostic One. [TREARS STUDIES II]), which is not on this map. Cited by 10 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
The Validity of a Novel Diabetes Diagnostic Device and Its Feasibility as Metabolic Syndrome Diagnostic One. [TREARS STUDIES II]
Who cites it
10 citing papers in PubMed.
- XSuLT: a web server for structural annotation and representation of sequence-structure alignments.Nucleic acids research · 2017Article
- Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.Chemical reviews · 2016Review
- Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences.Frontiers in microbiology · 2015Article
- Regional effects on chimera formation in 454 pyrosequenced amplicons from a mock community.Journal of microbiology (Seoul, Korea) · 2014Article
- H2rs: deducing evolutionary and functionally important residue positions by means of an entropy and similarity based analysis of multiple sequence alignments.BMC bioinformatics · 2014Article
- L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier.PloS one · 2012Article
- Novel biphenyl-oxidizing bacteria and dioxygenase genes from a korean tidal mudflat.Applied and environmental microbiology · 2011Article
- Sequence conservation in the prediction of catalytic sites.The protein journal · 2011Article
- A comparative study of conservation and variation scores.BMC bioinformatics · 2010Article
- Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment.The ISME journal · 2010Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Evolutionary conservation derived from a multiple sequence alignment is a powerful indicator of the functional significance of a residue, and it can help to predict active sites, ligand-binding sites, and protein interaction interfaces. The results of the existing algorithms in identifying the residue's conservation strongly depend on the sequence alignment, making the results highly variable. Here, by introducing the amino acid similarity matrix, we propose a novel gap-treating approach by combining the evolutionary information and von Neumann entropies to compute the residue conservation scores. It is indicated through a series of tested results that the new approach is quite encouraging and promising and may become a useful tool in complementing the existing methods.
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