(Q33415053)

26 July 2017

title

Computing highly correlated positions using mutual information and graph theory for G protein-coupled receptors (English)

1 reference

G protein-coupled receptor

26 July 2017

main subject

0 references

author

Sarosh Noshir Fatakia

object named as

Sarosh N Fatakia

series ordinal

1

0 references

Stefano Costanzi

object named as

Stefano Costanzi

series ordinal

2

0 references

author name string

Carson C Chow

series ordinal

3

1 reference

26 July 2017

language of work or name

English

0 references

publication date

5 March 2009

1 reference

26 July 2017

1 reference

26 July 2017

volume

4

1 reference

26 July 2017

issue

3

1 reference

26 July 2017

page(s)

e4681

1 reference

Creative Commons CC0 License

26 July 2017

copyright license

start time

5 March 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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Structure of a beta1-adrenergic G-protein-coupled receptor

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Mapping the UDP-glucuronic acid binding site in UDP-glucuronosyltransferase-1A10 by homology-based modeling: confirmation with biochemical evidence

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A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor

21 June 2018

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On the applicability of GPCR homology models to computer-aided drug discovery: a comparison between in silico and crystal structures of the beta2-adrenergic receptor.

21 June 2018

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

21 June 2018

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21 June 2018

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High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

21 June 2018

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GPCR engineering yields high-resolution structural insights into beta2-adrenergic receptor function

21 June 2018

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Crystal structure of the human beta2 adrenergic G-protein-coupled receptor

21 June 2018

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Functional specificity lies within the properties and evolutionary changes of amino acids

21 June 2018

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Identification of residues important for agonist recognition and activation in GPR40

21 June 2018

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Bidirectional, iterative approach to the structural delineation of the functional "chemoprint" in GPR40 for agonist recognition

21 June 2018

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21 June 2018

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Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives

21 June 2018

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Chemogenomics: structuring the drug discovery process to gene families.

21 June 2018

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Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions

21 June 2018

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Evaluation of small-molecule modulators of the luteinizing hormone/choriogonadotropin and thyroid stimulating hormone receptors: structure-activity relationships and selective binding patterns

21 June 2018

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A missense mutation in the seven-transmembrane domain of the human Ca2+ receptor converts a negative allosteric modulator into a positive allosteric modulator

21 June 2018

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Chemogenomics approaches to G-protein coupled receptor lead finding.

21 June 2018

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A low molecular weight agonist signals by binding to the transmembrane domain of thyroid-stimulating hormone receptor (TSHR) and luteinizing hormone/chorionic gonadotropin receptor (LHCGR).

21 June 2018

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Computational approaches to model ligand selectivity in drug design.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Determination of network of residues that regulate allostery in protein families using sequence analysis

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Human P2Y(6) receptor: molecular modeling leads to the rational design of a novel agonist based on a unique conformational preference.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Natural-like function in artificial WW domains

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Evolutionary information for specifying a protein fold

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Predicting specificity-determining residues in two large eukaryotic transcription factor families

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Networks of coevolving sites in structural and functional domains of serpin proteins.

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Architecture of P2Y nucleotide receptors: structural comparison based on sequence analysis, mutagenesis, and homology modeling.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Sequential binding of agonists to the beta2 adrenoceptor. Kinetic evidence for intermediate conformational states

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Amino acids determining enzyme-substrate specificity in prokaryotic and eukaryotic protein kinases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

GPCRDB information system for G protein-coupled receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Evolutionarily conserved networks of residues mediate allosteric communication 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=2650788

The mutual information: detecting and evaluating dependencies between variables.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Drug design strategies for targeting G-protein-coupled receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Seven-transmembrane receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Identification of G protein-coupled receptor genes from the human genome sequence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Evidence for distinct cation and calcimimetic compound (NPS 568) recognition domains in the transmembrane regions of the human Ca2+ receptor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Positive allosteric modulators of metabotropic glutamate 1 receptor: characterization, mechanism of action, and binding site

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Structural mimicry in G protein-coupled receptors: implications of the high-resolution structure of rhodopsin for structure-function analysis of rhodopsin-like receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

BAY36-7620: a potent non-competitive mGlu1 receptor antagonist with inverse agonist activity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Crystal structure of rhodopsin: A G protein-coupled receptor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Co-evolution of proteins with their interaction partners

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Correlations among amino acid sites in bHLH protein domains: an information theoretic 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=2650788

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=2650788

Ser203 as well as Ser204 and Ser207 in fifth transmembrane domain of the human beta2-adrenoceptor contributes to agonist binding and receptor activation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Role of the extracellular loops of G protein-coupled receptors in ligand recognition: a molecular modeling study of the human P2Y1 receptor.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

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=2650788

CPCCOEt, a noncompetitive metabotropic glutamate receptor 1 antagonist, inhibits receptor signaling without affecting glutamate binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

A graphical interface for correlated mutations and other protein structure prediction 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=2650788

Reading of DNA sequence logos: prediction of major groove binding by information theory

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Glutamate residues in the second extracellular loop of the human A2a adenosine receptor are required for ligand recognition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

An evolutionary trace method defines binding surfaces common to 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=2650788

Covariation of residues in the homeodomain sequence family

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic 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=2650788

How frequent are correlated changes in families of protein sequences?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Compensating changes in protein multiple sequence 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=2650788

Role of the second extracellular loop of adenosine receptors in agonist and antagonist binding. Analysis of chimeric A1/A3 adenosine receptors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

A method to predict functional residues 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=2650788

Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Correlation of co-ordinated amino acid substitutions with function in viruses related to tobacco mosaic virus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Structural basis of beta-adrenergic receptor function.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Inferring consensus structure from nucleic acid sequences.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis 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=2650788

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

A two-entropies analysis to identify functional positions in the transmembrane region of class A G protein-coupled receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Contacts between extracellular loop two and transmembrane helix six determine basal activity of the thyroid-stimulating hormone receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

A Mathematical Theory of Communication

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Positional dependence, cliques, and predictive motifs in the bHLH protein domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

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.0004681

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.0004681

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Analysis and prediction of functional sub-types from protein sequence alignments.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Covariation of amino acid positions in HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

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.0004681

Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

3-D-QSAR/CoMFA and recognition models of benzimidazole derivatives at the 5-HT(4) receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

[3H]Org 43553, the first low-molecular-weight agonistic and allosteric radioligand for the human luteinizing hormone receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Calindol, a positive allosteric modulator of the human Ca(2+) receptor, activates an extracellular ligand-binding domain-deleted rhodopsin-like seven-transmembrane structure in the absence of Ca(2+).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Graphical models of residue coupling in protein families.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Tracing evolutionary pressure

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Predicting functionally important residues from sequence conservation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Detecting coevolving amino acid sites using Bayesian mutational mapping

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

A model-based approach for detecting coevolving positions in a molecule.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Identification of functional surfaces of the zinc binding domains of intracellular receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Identification of functionally conserved residues with the use of entropy-variability plots

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

PCOAT: positional correlation analysis using multiple methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Lipid-facing correlated mutations and dimerization in G-protein coupled receptors

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0004681

Revealing the set of mutually correlated positions for the protein families of immunoglobulin fold.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2650788

A chemogenomic analysis of the transmembrane binding cavity of human G-protein-coupled receptors

31 October 2018

1 reference

12 December 2020

Sequence analysis reveals how G protein-coupled receptors transduce the signal to the G protein

1 reference

12 December 2020

Defining the nucleotide binding sites of P2Y receptors using rhodopsin-based homology modeling

1 reference

12 December 2020

Evaluation of a novel method for the identification of coevolving protein residues

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12 December 2020

Full correlation analysis of conformational protein dynamics

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12 December 2020

Detection and reduction of evolutionary noise in correlated mutation analysis

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12 December 2020

Multiple residues in the second extracellular loop are critical for M3 muscarinic acetylcholine receptor activation

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12 December 2020

Evolutionary constraint networks in ligand-binding domains: an information-theoretic approach

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12 December 2020

Structural biology: form and function instructions

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12 December 2020

The non-competitive antagonists 2-methyl-6-(phenylethynyl)pyridine and 7-hydroxyiminocyclopropan[b]chromen-1a-carboxylic acid ethyl ester interact with overlapping binding pockets in the transmembrane region of group I metabotropic glutamate recepto

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12 December 2020

Exploiting the co-evolution of interacting proteins to discover interaction specificity

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12 December 2020

10.1371/JOURNAL.PONE.0004681

Identifiers

DOI

1 reference

26 July 2017

0 references

1 reference

26 July 2017

1 reference