(Q30421148)

14 October 2017

Modeling coding-sequence evolution within the context of residue solvent accessibility (English)

1 reference

14 October 2017

3

1 reference

PubMed publication ID

21 June 2017

Austin G Meyer

2

0 references

author name string

Michael P Scherrer

series ordinal

1

1 reference

14 October 2017

12 September 2012

1 reference

14 October 2017

BMC Evolutionary Biology

1 reference

14 October 2017

12

1 reference

14 October 2017

179

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-12-179

14 October 2017

0 references

cites work

Integrating sequence variation and protein structure to identify sites under selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The relationship between relative solvent accessibility and evolutionary rate in protein evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Translationally optimal codons associate with aggregation-prone sites in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

CodonTest: modeling amino acid substitution preferences in coding sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Benchmarking multi-rate codon models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Evolutionary fingerprinting of genes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Translationally optimal codons associate with structurally sensitive sites in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Contact density affects protein evolutionary rate from bacteria to animals.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

A "silent" polymorphism in the MDR1 gene changes substrate specificity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Assessing site-interdependent phylogenetic models of sequence evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Structural determinants of the rate of protein evolution in yeast.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Protein stability promotes evolvability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Why highly expressed proteins evolve slowly

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Loss of protein structure stability as a major causative factor in monogenic disease.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Site-to-site variation of synonymous substitution rates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

HyPhy: hypothesis testing using phylogenies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

MUSCLE: multiple sequence alignment with high accuracy and high throughput

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The problem of counting sites in the estimation of the synonymous and nonsynonymous substitution rates: implications for the correlation between the synonymous substitution rate and codon usage bias

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Protein evolution with dependence among codons due to tertiary structure.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The pattern of amino acid replacements in alpha/beta-barrels

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Silent mutations affect in vivo protein folding in Escherichia coli

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Codon-substitution models for heterogeneous selection pressure at amino acid sites

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

20 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Dissecting the regulatory circuitry of a eukaryotic genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

SGD: Saccharomyces Genome Database

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Ribosome-mediated translational pause and protein domain organization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Context-dependent optimal substitution matrices

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

A codon-based model of nucleotide substitution for protein-coding DNA sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The relation between the divergence of sequence and structure in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

The rapid generation of mutation data matrices from protein sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Combining protein evolution and secondary structure

20 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Computational methods for evaluating phylogenetic models of coding sequence evolution with dependence between codons.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Solvent exposure imparts similar selective pressures across a range of yeast proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Multimodel Inference: Understanding AIC and BIC in Model Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Modeling amino acid substitution patterns in orthologous and paralogous genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Transient ribosomal attenuation coordinates protein synthesis and co-translational folding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

Understanding hierarchical protein evolution from first principles 1 1Edited by J. Thornton

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1471-2148-12-179

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3527230

Models of natural mutations including site heterogeneity

26 November 2018

1 reference

12 December 2020

Structural determinants of protein evolution are context-sensitive at the residue level

1 reference

12 December 2020

Protein structural influences in rhodopsin evolution

1 reference

12 December 2020

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

12 December 2020

Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

1 reference

12 December 2020

Synonymous codon substitutions affect ribosome traffic and protein folding during in vitro translation

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-12-179

1 reference

Dimensions Publication ID

14 October 2017

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2148-12-179

1 reference

14 October 2017

PubMed publication ID

22967129

1 reference