(Q35544008)

8 August 2017

title

Too packed to change: side-chain packing and site-specific substitution rates in protein evolution (English)

1 reference

8 August 2017

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Julian Echave

2

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author name string

María Laura Marcos

series ordinal

1

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8 August 2017

language of work or name

1 reference

23 April 2015

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8 August 2017

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8 August 2017

volume

3

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8 August 2017

page(s)

e911

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Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites

8 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Predicting evolutionary site variability from structure in viral proteins: buriedness, packing, flexibility, and design.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Biophysics of protein evolution and evolutionary protein biophysics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Local packing density is the main structural determinant of the rate of protein sequence evolution at site level

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Maximum allowed solvent accessibilites of residues in proteins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

The interface of protein structure, protein biophysics, and molecular evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Evolutionary information hidden in a single protein structure

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Protein elastic network models and the ranges of cooperativity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Deriving protein dynamical properties from weighted protein contact number.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

MAFFT version 5: improvement in accuracy of multiple sequence alignment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4411540

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

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25922797

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A perturbative view of protein structural variation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25922797

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.7717/PEERJ.911

1 reference

8 August 2017

1 reference

8 August 2017

1 reference