(Q31042817)

16 October 2017

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

1 reference

species distribution model

16 October 2017

0 references

0 references

1 reference

1

1 reference

16 October 2017

4

Michele Vendruscolo

1 reference

16 October 2017

Markus Porto

2

1 reference

16 October 2017

H Eduardo Roman

series ordinal

3

1 reference

16 October 2017

31 May 2006

1 reference

16 October 2017

BMC Evolutionary Biology

1 reference

16 October 2017

6

1 reference

16 October 2017

43

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-6-43

16 October 2017

0 references

cites work

Evolutionary information for specifying a protein fold

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

The application of statistical physics to evolutionary biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Adaptive evolution of transcription factor binding sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

The structurally constrained protein evolution model accounts for sequence patterns of the LbetaH superfamily

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Protein folding and misfolding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Protein evolution with dependence among codons due to tertiary structure.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Why are proteins so robust to site mutations?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

How to guarantee optimal stability for most representative structures in the Protein Data Bank.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Quantitative comparison of the ability of hydropathy scales to recognize surface beta-strands in proteins.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Roles of molecular chaperones in cytoplasmic protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Neutral evolution of mutational robustness

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Hsp90 as a capacitor for morphological evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

On the thermodynamic hypothesis of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

How evolution makes proteins fold quickly

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

How are model protein structures distributed in sequence space?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Asymmetric substitution patterns in the two DNA strands of bacteria

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Smoothness within ruggedness: the role of neutrality in adaptation.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Enlarged representative set of protein structures

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Boltzmann-like statistics of protein architectures. Origins and consequences.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolution-like selection of fast-folding model proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

A simple method for displaying the hydropathic character of a protein

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolutionary Rate at the Molecular Level

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Spin glasses and the statistical mechanics of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Compositional constraints and genome evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Optimal protein-folding codes from spin-glass theory

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Role of very slightly deleterious mutations in molecular evolution and polymorphism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

A simplified representation of protein conformations for rapid simulation of protein folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Principal eigenvector of contact matrices and hydrophobicity profiles in proteins

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Genomic determinants of protein folding thermodynamics in prokaryotic organisms.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Molecular clock in neutral protein evolution

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Reconstruction of protein structures from a vectorial representation

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Statistical properties of neutral evolution

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Quantifying the effect of burial of amino acid residues on protein stability

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Connectivity of Neutral Networks, Overdispersion, and Structural Conservation in Protein Evolution

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Lack of self-averaging in neutral evolution of proteins

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Endosymbiotic bacteria: groEL buffers against deleterious mutations

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Energetics, stability, and prediction of transmembrane helices

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolutionarily conserved pathways of energetic connectivity in protein families

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Testing a new Monte Carlo algorithm for protein folding

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolution of model proteins on a foldability landscape.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Intrastrand parity rules of DNA base composition and usage biases of synonymous codons.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

From sequences to shapes and back: a case study in RNA secondary structures.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Evolutionary trees from DNA sequences: A maximum likelihood approach

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1570368

Site interdependence attributed to tertiary structure in amino acid sequence evolution

25 November 2018

1 reference

12 December 2020

The distribution of structures in evolving protein populations

1 reference

12 December 2020

Continuity in evolution: on the nature of transitions

1 reference

12 December 2020

On the constancy of the evolutionary rate of cistrons

1 reference

12 December 2020

Hydrophobic character of amino acid residues in globular proteins

1 reference

12 December 2020

Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds

1 reference

12 December 2020

Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach

1 reference

12 December 2020

Optimal local propensities for model proteins

1 reference

12 December 2020

Factors governing the foldability of proteins

1 reference

12 December 2020

Influence of genomic G+C content on average amino-acid composition of proteins from 59 bacterial species

1 reference

12 December 2020

Models of natural mutations including site heterogeneity

1 reference

12 December 2020

Directional mutational pressure affects the amino acid composition and hydrophobicity of proteins in bacteria

1 reference

12 December 2020

Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes

1 reference

12 December 2020

Universal replication biases in bacteria

1 reference

12 December 2020

Structural constraints and emergence of sequence patterns in protein evolution

1 reference

12 December 2020

A universal trend of amino acid gain and loss in protein evolution

1 reference

12 December 2020

Identifiers

DOI

10.1186/1471-2148-6-43

1 reference

Dimensions Publication ID

16 October 2017

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1471-2148-6-43

1 reference

16 October 2017

PubMed publication ID

16737532

1 reference