Works (4)

Updated: July 5th, 2023 15:54

2009 journal article

Estimates of natural selection due to protein tertiary structure inform the ancestry of biallelic loci

Gene, 441(1-2), 45–52.

By: S. Choi n, E. Stone n, H. Kishino* & J. Thorne n

MeSH headings : Evolution, Molecular; Gene Frequency; Humans; Polymorphism, Single Nucleotide; Protein Structure, Tertiary; Proteins / genetics; Selection, Genetic
TL;DR: This work focuses on 140 nonsynonymous single nucleotide polymorphisms of humans that are in proteins with known tertiary structures and finds that the technique for employing protein tertiary structure information yields some biologically plausible results but that it does not substantially improve the inference of ancestral human allele types. (via Semantic Scholar)
Source: NC State University Libraries
Added: August 6, 2018

2008 journal article

Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences


By: S. Choi n, B. Redelings n & J. Thorne n

author keywords: variable-length Markov model; profile hidden Markov model; insertion-deletion model; scaled selection coefficient; fitness; Pfam
MeSH headings : Computer Simulation; DNA / genetics; Evolution, Molecular; Genetics, Population; INDEL Mutation / genetics; Markov Chains; Models, Genetic; Population Density; Proteins / genetics; Selection, Genetic
TL;DR: This work explores how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions, and introduces an insertion–deletion model that describes selectively neutral evolutionary changes to DNA. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Population genetics without intraspecific data


author keywords: dependence among sites; fixation probability; protein structure; RNA structure
MeSH headings : Animals; Annexin A5 / genetics; Computational Biology; Computer Simulation; Evolution, Molecular; Genetic Variation; Genetics, Population; Likelihood Functions; Mice; Models, Biological; Models, Genetic; Nucleic Acid Conformation; Phenotype; Phylogeny; RNA / chemistry; RNA / genetics; Rats; Selection, Genetic
TL;DR: It is argued that statistical fit to data should not be the sole criterion for assessing models of sequence change, and a good interspecific model should also yield a clear and biologically plausible population genetic interpretation. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

2007 journal article

Quantifying the impact of protein tertiary structure on molecular evolution


By: S. Choi n, A. Hobolth n, D. Robinson n, H. Kishino* & J. Thorne n

author keywords: molecular evolution; protein structure impact; Gene Ontology; MCMC; Bayes factor
MeSH headings : Bayes Theorem; Computational Biology; Computer Simulation; Data Interpretation, Statistical; Evolution, Molecular; Protein Structure, Tertiary; Proteins / chemistry; Proteins / genetics; Sequence Alignment
TL;DR: Although their influences on rates of evolution vary among protein families, it is found that the mean impacts of solvent accessibility and pairwise interactions are about the same. (via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018

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