(Q30376006)

19 August 2017

Translationally optimal codons associate with structurally sensitive sites in proteins (English)

1 reference

19 August 2017

3

1 reference

19 August 2017

1

1 reference

30 October 2018

Mason Weems

2

1 reference

19 August 2017

6 April 2009

1 reference

Molecular Biology and Evolution

19 August 2017

1 reference

19 August 2017

26

1 reference

19 August 2017

1571-1580

1 reference

19 August 2017

7

1 reference

Conflicting selection pressures on synonymous codon use in yeast suggest selection on mRNA secondary structures

19 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Mistranslation-induced protein misfolding as a dominant constraint on coding-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=2734146

Analysis of the distribution of functionally relevant rare codons

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Structural mapping of protein interactions reveals differences in evolutionary pressures correlated to mRNA level and protein abundance

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

The selection of acceptable protein mutations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

The stability effects of protein mutations appear to be universally distributed

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Tissue-specific differences in human transfer RNA expression

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

Genetics. SNPs, silent but not invisible.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring 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=2734146

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Selection acts on DNA secondary structures to decrease transcriptional mutagenesis

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

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=2734146

Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Thermodynamic prediction of protein neutrality

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Protein tolerance to random amino acid change

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Integrating high-throughput and computational data elucidates bacterial networks

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

A gene atlas of the mouse and human protein-encoding transcriptomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Statistical aspects of the analysis of data from retrospective studies of 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=2734146

The signature of selection mediated by expression on human 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=2734146

Conserved residue clustering and protein structure prediction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

DNA helix: the importance of being GC-rich

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Evolution of synonymous codon usage in metazoans

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

A simple physical model for binding energy hot spots in protein-protein complexes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

GTOP: a database of protein structures predicted from genome 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=2734146

Protein folding theory: from lattice to all-atom 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=2734146

PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

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=2734146

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=2734146

The relationship between synonymous codon usage and protein 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=2734146

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=2734146

Codon usage bias and tRNA abundance in Drosophila

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

CATH--a hierarchic classification of protein domain structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Maximizing transcription efficiency causes 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=2734146

Protein secondary structural types are differentially coded on messenger RNA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

An evolutionary trace method defines binding surfaces common to protein families

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

Structural and genetic analysis of protein stability

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

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=2734146

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Codon usage and tRNA content in unicellular and multicellular organisms

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed 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=2734146

Translational selection and molecular evolution

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

A single determinant dominates the rate of yeast protein evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as "spacers" which do not require a specific sequence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Evolutionary conservation of the folding nucleus.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Tracing specific synonymous codon-secondary structure correlations through evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Specific correlations between relative synonymous codon usage and protein secondary structure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

A gene expression map for the euchromatic genome of Drosophila melanogaster.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Codon bias as a factor in regulating expression via translation rate in the human genome.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Computational alanine scanning of protein-protein interfaces

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Highly expressed genes in yeast evolve slowly.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2734146

Evidence for Purifying Selection Against Synonymous Mutations in Mammalian Exonic Splicing Enhancers

26 November 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSP070

Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species

21 January 2018

1 reference

12 December 2020

Unifying measures of gene function and evolution

1 reference

12 December 2020

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

1 reference

12 December 2020

Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSP070

1 reference

19 August 2017

1 reference

19 August 2017

1 reference

PMCID

2734146