A new ensemble coevolution system for detecting HIV-1 protein coevolution. (Q35094794)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25564011 AND SRC:MED&resulttype=core&format=json

27 February 2020

title

A new ensemble coevolution system for detecting HIV-1 protein coevolution (English)

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27 February 2020

0 references

9

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Andrea-Clemencia Pineda-Peña

27 February 2020

4

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27 February 2020

Ricardo Khouri

5

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27 February 2020

Mónica Eusébio

7

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27 February 2020

author name string

Guangdi Li

1

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27 February 2020

Kristof Theys

2

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27 February 2020

Jens Verheyen

3

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27 February 2020

Supinya Piampongsant

6

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27 February 2020

Jan Ramon

8

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27 February 2020

publication date

7 January 2015

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27 February 2020

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27 February 2020

volume

10

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27 February 2020

page(s)

1

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Creative Commons Attribution 4.0 International

27 February 2020

copyright license

start time

7 January 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Computational identification of novel amino-acid interactions in HIV Gag via correlated evolution.

9 July 2018

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Human Immunodeficiency Virus Gag and protease: partners in resistance

9 July 2018

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Deep architectures for protein contact map prediction

9 July 2018

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9 July 2018

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9 July 2018

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Sequence evolution correlates with structural dynamics

9 July 2018

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Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease

9 July 2018

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

9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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9 July 2018

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

9 July 2018

1 reference

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Structural Convergence between Cryo-EM and NMR Reveals Intersubunit Interactions Critical for HIV-1 Capsid Function

9 July 2018

1 reference

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9 July 2018

1 reference

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Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Protein sectors: evolutionary units of three-dimensional structure

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

X-ray structures of the hexameric building block of the HIV capsid

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

NNcon: improved protein contact map prediction using 2D-recursive neural networks

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Analysis of correlated mutations in HIV-1 protease using spectral clustering

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Detecting groups of coevolving positions in a molecule: a clustering approach

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Detecting coevolution in and among protein domains

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

HIV-1 subtype B protease and reverse transcriptase amino acid covariation

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Specificity in protein interactions and its relationship with sequence diversity and coevolution

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Improved residue contact prediction using support vector machines and a large feature set.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Super learning: an application to the prediction of HIV-1 drug resistance

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Conformation of the HIV-1 Gag protein in solution.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

A protein domain interaction interface database: InterPare

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Learning multiple evolutionary pathways from cross-sectional data

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Evolutionarily conserved networks of residues mediate allosteric communication in proteins

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Characterization of a putative alpha-helix across the capsid-SP1 boundary that is critical for the multimerization of human immunodeficiency virus type 1 gag.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Substrate shape determines specificity of recognition for HIV-1 protease: analysis of crystal structures of six substrate complexes

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Evolutionarily conserved pathways of energetic connectivity in protein families

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Reversion of a human immunodeficiency virus type 1 matrix mutation affecting Gag membrane binding, endogenous reverse transcriptase activity, and virus infectivity

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Detection of a trimeric human immunodeficiency virus type 1 Gag intermediate is dependent on sequences in the matrix protein, p17.

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Errors in protein structures

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Resistance pathways of human immunodeficiency virus type 1 against the combination of zidovudine and lamivudine

9 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Reducing phylogenetic bias in correlated mutation analysis

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

A new method for revealing correlated mutations under the structural and functional constraints in proteins

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

PconsC: combination of direct information methods and alignments improves contact prediction

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

A Study of the Coevolutionary Patterns Operating within the env Gene of the HIV-1 Group M Subtypes

8 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4332441

8 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25564011

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13062-014-0031-8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25564011 AND SRC:MED&resulttype=core&format=json

Dimensions Publication ID

27 February 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25564011 AND SRC:MED&resulttype=core&format=json

27 February 2020

PubMed publication ID

25564011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25564011 AND SRC:MED&resulttype=core&format=json