Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation (Q33623719)

28 July 2017

title

Identifying and seeing beyond multiple sequence alignment errors using intra-molecular protein covariation (English)

1 reference

28 July 2017

1 reference

Gregory B Gloor

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Russell J Dickson

1 reference

28 July 2017

Lindi M Wahl

series ordinal

1 reference

28 July 2017

Andrew D Fernandes

series ordinal

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28 July 2017

language of work or name

English

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publication date

28 June 2010

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28 July 2017

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28 July 2017

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28 July 2017

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28 July 2017

page(s)

e11082

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Creative Commons Attribution 4.0 International

28 July 2017

start time

28 June 2010

1 reference

April 2022 Public Data File from Crossref

copyrighted

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cites work

A unified genetic, computational and experimental framework identifies functionally relevant residues of the homing endonuclease I-BmoI.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Identification of coevolving residues and coevolution potentials emphasizing structure, bond formation and catalytic coordination in protein evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

CDD: specific functional annotation with the Conserved Domain Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Protein co-evolution, co-adaptation and interactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Alignment uncertainty and genomic analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

An integrated system for studying residue coevolution in proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Accuracy of structure-based sequence alignment of automatic methods

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Multiple sequence alignment.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Evolutionary information for specifying a protein fold

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

PROTEIN STRUCTURE RELATIONSHIPS REVEALED BY MUTATIONAL ANALYSIS.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

21 June 2018

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0011082

Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Evolutionarily conserved pathways of energetic connectivity in protein families

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Coevolving protein residues: maximum likelihood identification and relationship to structure.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Cn3D: a new generation of three-dimensional molecular structure viewer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0011082

Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0011082

Using information theory to search for co-evolving residues in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0011082

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0011082

Functionally compensating coevolving positions are neither homoplasic nor conserved in clades

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Contact prediction using mutual information and neural nets

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

Functional coevolutionary networks of the Hsp70-Hop-Hsp90 system revealed through computational analyses

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2893159

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20596526

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0011082

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference