COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator. (Q36225597)

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30 March 2020

title

COUSCOus: improved protein contact prediction using an empirical Bayes covariance estimator (English)

1 reference

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30 March 2020

1

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30 March 2020

Raghvendra Mall

2

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30 March 2020

author name string

Khalid Kunji

3

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30 March 2020

Mohammed El Anbari

4

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30 March 2020

Michael Aupetit

5

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30 March 2020

Ehsan Ullah

6

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30 March 2020

Halima Bensmail

7

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30 March 2020

publication date

15 December 2016

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30 March 2020

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30 March 2020

volume

17

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30 March 2020

issue

1

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30 March 2020

page(s)

533

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Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning

30 March 2020

cites work

1 reference

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CASP11 refinement experiments with ROSETTA.

1 October 2017

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MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins

1 October 2017

1 reference

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Sequence co-evolution gives 3D contacts and structures of protein complexes

1 October 2017

1 reference

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PconsFold: improved contact predictions improve protein models

1 October 2017

1 reference

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Evol and ProDy for bridging protein sequence evolution and structural dynamics

1 October 2017

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Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.

1 October 2017

1 reference

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FreeContact: fast and free software for protein contact prediction from residue co-evolution

1 October 2017

1 reference

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De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

1 October 2017

1 reference

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Pfam: the protein families database

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Emerging methods in protein co-evolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Protein structure prediction from sequence variation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Predicting protein residue–residue contacts using deep networks and boosting

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Three-dimensional structures of membrane proteins from genomic sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Protein 3D structure computed from evolutionary sequence variation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Sparse inverse covariance estimation with the graphical lasso

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Assessment of intramolecular contact predictions for CASP7.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

PROTEIN STRUCTURE RELATIONSHIPS REVEALED BY MUTATIONAL ANALYSIS.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

1 October 2017

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Protein secondary structure prediction based on position-specific scoring matrices

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

1 October 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

1 October 2017

https://api.crossref.org/works/10.1186%2FS12859-016-1400-3

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Interpol: An R package for preprocessing of protein sequences

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

Bio3d: an R package for the comparative analysis of protein structures.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159955

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

22 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2FS12859-016-1400-3

10.1186/S12859-016-1400-3

21 January 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27978812%20AND%20SRC:MED&resulttype=core&format=json

journals/bmcbi/RawiMKAAUB16

30 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27978812%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

PubMed publication ID

27978812

1 reference