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An Alternative Model of Amino Acid Replacement [PDF]
, 2004 The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution.
Altschul +27 more
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A metric model of amino acid substitution [PDF]
Bioinformatics, 2004 Abstract Motivation: We address the question of whether there exists an effective evolutionary model of amino-acid substitution that forms a metric-distance function. There is always a trade-off between speed and sensitivity among competing computational methods of determining sequence homology.
Weijia, Xu, Daniel P, Miranker
openaire +3 more sources
Further characterization of glycine-containing microcystins from the McMurdo Dry Valleys of Antarctica [PDF]
, 2015 Microcystins are hepatotoxic cyclic peptides produced by several cyanobacterial genera worldwide. In 2008, our research group identified eight new glycine-containing microcystin congeners in two hydro-terrestrial mat samples from the McMurdo Dry Valleys ...
Cary, S. Craig +5 more
core +3 more sources
PLoS ONE, 2011 BackgroundA mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over ...
Sanzo Miyazawa
doaj +1 more source
Benchmarking multi-rate codon models. [PDF]
PLoS ONE, 2010 The single rate codon model of non-synonymous substitution is ubiquitous in phylogenetic modeling. Indeed, the use of a non-synonymous to synonymous substitution rate ratio parameter has facilitated the interpretation of selection pressure on genomes ...
Wayne Delport +4 more
doaj +1 more source
Quaternary structure is an essential component that contributes to the sophisticated allosteric regulation mechanism in a key enzyme from Mycobacterium tuberculosis. [PDF]
PLoS ONE, 2017 The first enzyme of the shikimate pathway, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), adopts a range of distinct allosteric regulation mechanisms in different organisms, related to different quaternary assemblies.
Wanting Jiao +3 more
doaj +1 more source
Selection on Amino Acid Substitutions in Arabidopsis [PDF]
Molecular Biology and Evolution, 2008 Studies of nucleotide diversity have found an excess of low-frequency amino acid polymorphisms segregating in Arabidopsis thaliana, suggesting a predominance of weak purifying selection acting on amino acid polymorphism in this inbreeding species.
John Paul, Foxe +5 more
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Rate variation during molecular evolution: creationism and the cytochrome c molecular clock [PDF]
, 2017 Molecular clocks based upon amino acid sequences in proteins have played a major role in the clarification of evolutionary phylogenies. Creationist criticisms of these methods sometimes rely upon data that might initially seem to be paradoxical.
Hofmann James, R.
core +1 more source
Bayesian analysis of amino acid substitution models [PDF]
Philosophical Transactions of the Royal Society B: Biological Sciences, 2008 Models of amino acid substitution present challenges beyond those often faced with the analysis of DNA sequences. The alignments of amino acid sequences are often small, whereas the number of parameters to be estimated is potentially large when compared with the number of free parameters for nucleotide substitution models.
John P, Huelsenbeck +3 more
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Sequence-Based Analysis of Thermal Adaptation and Protein Energy Landscapes in an Invasive Blue Mussel (Mytilus galloprovincialis). [PDF]
, 2017 Adaptive responses to thermal stress in poikilotherms plays an important role in determining competitive ability and species distributions. Amino acid substitutions that affect protein stability and modify the thermal optima of orthologous proteins may ...
Kober, Kord M +3 more
core +1 more source