(Q30353641)

25 September 2017

Protein evolution along phylogenetic histories under structurally constrained substitution models. (English)

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25 September 2017

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1

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25 September 2017

3

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25 September 2017

Ugo Bastolla

4

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author name string

Helena G Dos Santos

series ordinal

2

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PMC publication ID

5221705

25 September 2017

language of work or name

English

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publication date

12 September 2013

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25 September 2017

9

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inferred from page(s)

published in

Bioinformatics

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25 September 2017

29

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25 September 2017

23

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25 September 2017

3020-3028

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Computer programs and methodologies for the simulation of DNA sequence data with recombination

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Frustration in the energy landscapes of multidomain protein misfolding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Bringing molecules back into molecular evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Simulation of molecular data under diverse evolutionary scenarios

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Amino acid coevolution induces an evolutionary Stokes shift.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Protein conformational diversity modulates sequence divergence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Computer simulations: tools for population and evolutionary genetics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Biophysical and structural considerations for protein sequence evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Quantifying the impact of dependent evolution among sites in phylogenetic inference

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Mutation bias favors protein folding stability in the evolution of small populations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

The effect of recombination on the reconstruction of ancestral sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Trade-off between positive and negative design of protein stability: from lattice models to real proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Coalescent simulation of intracodon recombination

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Identifying the important HIV-1 recombination breakpoints.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Comparative protein structure modeling using Modeller

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Engineering by homologous recombination: exploring sequence and function within a conserved fold

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

The quest for natural selection in the age of comparative genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Positive and negative design in stability and thermal adaptation of natural proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Statistical potential for assessment and prediction of protein structures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Evaluation of models for the evolution of protein sequences and functions under structural constraint

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

A protein evolution model with independent sites that reproduces site-specific amino acid distributions from the Protein Data Bank

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Divergence, recombination and retention of functionality during protein evolution.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

The application of statistical physics to evolutionary biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

ProtTest: selection of best-fit models of protein evolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

A coalescent model of recombination hotspots

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Approximate Bayesian computation in population genetics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Recombination in evolutionary genomics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Why are proteins so robust to site mutations?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Comparative protein structure modeling of genes and genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Models of molecular evolution and phylogeny

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Recovery of protein structure from contact maps

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Gene genealogies within mutant allelic classes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Comparative protein modelling by satisfaction of spatial restraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5221705

Statistical properties of neutral evolution

3 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Accurate estimation of substitution rates with neighbor-dependent models in a phylogenetic context.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Population size and fragmentation thresholds for the maintenance of genetic diversity in the herbaceous endemic Scutellaria montana (Lamiaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Random-energy model: An exactly solvable model of disordered systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

The evolution and evolutionary consequences of marginal thermostability in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Protein conformational diversity correlates with evolutionary rate.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Protein misfolding: optional barriers, misfolded intermediates, and pathway heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Models of Molecular Evolution and Phylogeny: Table 1

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Detecting selection for negative design in proteins through an improved model of the misfolded state

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Offspring fitness in relation to population size and genetic variation in the rare perennial plant species Gentiana pneumonanthe (Gentianaceae).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

The effect of branch length variation on the selection of models of molecular evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Neutral evolution of model proteins: diffusion in sequence space and overdispersion

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Stability constraints and protein evolution: the role of chain length, composition and disulfide bonds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIOINFORMATICS%2FBTT530

Recombination and the molecular clock

21 January 2018

1 reference

12 December 2020

Structural constraints and emergence of sequence patterns in protein evolution

1 reference

12 December 2020

Why are proteins marginally stable?

1 reference

12 December 2020

Site interdependence attributed to tertiary structure in amino acid sequence evolution

1 reference

12 December 2020

Properties of a neutral allele model with intragenic recombination

1 reference

12 December 2020

10.1093/BIOINFORMATICS/BTT530

Identifiers

DOI

1 reference

journals/bioinformatics/ArenasSPB13

25 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PMC publication ID

5221705

25 September 2017

PubMed publication ID

24037213

1 reference

PMC publication ID

5221705