Divergence, recombination and retention of functionality during protein evolution. (Q30351513)

12 October 2017

Divergence, recombination and retention of functionality during protein evolution. (English)

1 reference

12 October 2017

0 references

4

1 reference

12 October 2017

Yanlong O Xu

1

1 reference

12 October 2017

Randall W Hall

series ordinal

2

1 reference

12 October 2017

Richard A Goldstein

series ordinal

3

1 reference

12 October 2017

1 September 2005

1 reference

12 October 2017

1 reference

12 October 2017

2

1 reference

12 October 2017

3

1 reference

12 October 2017

158-167

1 reference

Context dependence and coevolution among amino acid residues in proteins.

12 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Protein structure and evolutionary history determine sequence space topology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Detecting gradients of asymmetry in site-specific substitutions in mitochondrial 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=2943960

Analysis of among-site variation in substitution patterns

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional 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=2943960

Genomic biodiversity, phylogenetics and coevolution in 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=2943960

Perspectives on protein evolution from simple exact 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=2943960

Early bioinformatics: the birth of a discipline--a personal view

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Likelihood Analysis of Asymmetrical Mutation Bias Gradients in Vertebrate Mitochondrial 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=2943960

An improved protein decoy set for testing energy functions for protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Information content of molecular 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=2943960

A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Discrimination of native protein structures using atom-atom contact scoring

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Is sparse taxon sampling a problem for 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=2943960

Thoroughly sampling sequence space: large-scale protein design of structural ensembles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Increased taxon sampling is advantageous for 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=2943960

Topological determinants of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Protein building blocks preserved by 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=2943960

Ab initio protein structure prediction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

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=2943960

Review: protein secondary structure prediction continues to rise.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

A distance-dependent atomic knowledge-based potential for improved protein structure selection.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Evolution of functionality in lattice 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=2943960

Ab initio protein structure prediction: progress and prospects.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Assessing an unknown evolutionary process: effect of increasing site-specific knowledge through taxon addition.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Estimating the total number of protein folds

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Effect of alphabet size and foldability requirements on protein structure designability.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

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=2943960

Protein structure prediction by threading. Why it works and why it does not.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

On the thermodynamic hypothesis of protein folding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

How are model protein structures distributed in sequence space?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Principles of protein folding--a perspective from simple exact 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=2943960

Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?

3 June 2018

1 reference

https://api.crossref.org/works/10.1186%2F1479-7364-2-3-158

Evolution of model proteins on a foldability landscape.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1479-7364-2-3-158

Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1479-7364-2-3-158

MOPED: method for optimizing physical energy parameters using decoys.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1479-7364-2-3-158

Developing optimal non-linear scoring function for protein design

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1479-7364-2-3-158

Phylogenetic estimation of context-dependent substitution rates by maximum likelihood

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2943960

Models of natural mutations including site heterogeneity

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16197733

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The distribution of structures in evolving protein populations

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16197733

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifying proteins of high designability via surface-exposure patterns

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16197733

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1479-7364-2-3-158

1 reference

Dimensions Publication ID

12 October 2017

0 references

1 reference

12 October 2017

PubMed publication ID

16197733

1 reference