(Q34455146)

2 August 2017

title

Accurate simulation and detection of coevolution signals in multiple sequence alignments (English)

1 reference

2 August 2017

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1 reference

Elisabeth R. M. Tillier

object named as

Elisabeth R Tillier

series ordinal

2

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author name string

Sharon H Ackerman

series ordinal

1

1 reference

2 August 2017

Domenico L Gatti

series ordinal

3

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2 August 2017

language of work or name

English

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publication date

16 October 2012

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2 August 2017

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2 August 2017

volume

7

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2 August 2017

issue

10

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2 August 2017

page(s)

e47108

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Creative Commons Attribution 4.0 International

2 August 2017

copyright license

start time

16 October 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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6 July 2018

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Protein 3D structure computed from evolutionary sequence variation

6 July 2018

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Direct-coupling analysis of residue coevolution captures native contacts across many protein families

6 July 2018

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PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

6 July 2018

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Validation of coevolving residue algorithms via pipeline sensitivity analysis: ELSC and OMES and ZNMI, oh my!

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Disentangling direct from indirect co-evolution of residues in protein alignments

6 July 2018

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Protein sectors: evolutionary units of three-dimensional structure

6 July 2018

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6 July 2018

Chaperones of F1-ATPase

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

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Why should we care about molecular coevolution?

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Identification of direct residue contacts in protein-protein interaction by message passing

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

6 July 2018

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Testing Geometrical Discrimination within an Enzyme Active Site: Constrained Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

6 July 2018

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Reducing the false positive rate in the non-parametric analysis of molecular coevolution.

6 July 2018

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6 July 2018

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6 July 2018

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

6 July 2018

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SIMPROT: using an empirically determined indel distribution in simulations of protein evolution

6 July 2018

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Natural-like function in artificial WW domains

6 July 2018

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6 July 2018

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6 July 2018

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Evolutionarily conserved networks of residues mediate allosteric communication in proteins

6 July 2018

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Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations

6 July 2018

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MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

6 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Insights into the structure, solvation, and mechanism of ArsC arsenate reductase, a novel arsenic detoxification enzyme

6 July 2018

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Structure of an active soluble mutant of the membrane-associated (S)-mandelate dehydrogenase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Structure of the ArsA ATPase: the catalytic subunit of a heavy metal resistance pump

6 July 2018

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T-Coffee: A novel method for fast and accurate multiple sequence alignment

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Independent component analysis: algorithms and applications

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Structure and mechanism of 3-deoxy-D-manno-octulosonate 8-phosphate synthase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Effective use of sequence correlation and conservation in fold recognition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Evolutionarily conserved pathways of energetic connectivity in protein families

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

The mobile flavin of 4-OH benzoate hydroxylase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Structure and mechanism of the iron‐sulfur flavoprotein phthalate dioxygenase reductase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Functionally compensating coevolving positions are neither homoplasic nor conserved in clades

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Influence of conservation on calculations of amino acid covariance in multiple sequence alignments

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

Minimax mutual information approach for independent component analysis.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3473043

10.1371/JOURNAL.PONE.0047108

27 October 2018

Identifiers

DOI

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2 August 2017

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2 August 2017

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