First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin. (Q30340985)

19 September 2017

First principles predictions of the structure and function of g-protein-coupled receptors: validation for bovine rhodopsin. (English)

1 reference

G protein-coupled receptor

19 September 2017

0 references

protein function prediction

0 references

protein structure prediction

0 references

Nagarajan Vaidehi

1 reference

19 September 2017

0 references

Rene J Trabanino

1 reference

19 September 2017

Spencer E Hall

1 reference

19 September 2017

Wely B Floriano

1 reference

19 September 2017

Victor W T Kam

1 reference

19 September 2017

William A Goddard

1 reference

19 September 2017

language of work or name

English

0 references

publication date

1 April 2004

1 reference

19 September 2017

1 reference

19 September 2017

1 reference

19 September 2017

1 reference

19 September 2017

1904-1921

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

19 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Interaction of E. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Prediction of structure and function of G protein-coupled receptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

The structural basis of G-protein-coupled receptor function and dysfunction in human diseases

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Modeling the 3D structure of GPCRs from sequence

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Activation of rhodopsin: new insights from structural and biochemical studies

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Orphan G-protein coupled receptors: novel drug targets for the pharmaceutical industry

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structure. Rhodopsin sees the light

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Comparative protein structure modeling of genes and genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Crystal structure of rhodopsin: A G protein-coupled receptor

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structural organization of G-protein-coupled receptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Combinatorial receptor codes for odors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

A comparison of the efficiency of G protein activation by ligand-free and light-activated forms of rhodopsin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Automated method for modeling seven-helix transmembrane receptors from experimental data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structure and function of G protein-coupled receptors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

The hydrophobic moment detects periodicity in protein hydrophobicity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

WHAT IF: a molecular modeling and drug design program

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Basic local alignment search tool

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Mutagenesis and modelling of the alpha(1b)-adrenergic receptor highlight the role of the helix 3/helix 6 interface in receptor activation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structure and function in rhodopsin: mapping light-dependent changes in distance between residue 316 in helix 8 and residues in the sequence 60-75, covering the cytoplasmic end of helices TM1 and TM2 and their connection loop CL1.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structure and function in rhodopsin: mapping light-dependent changes in distance between residue 65 in helix TM1 and residues in the sequence 306-319 at the cytoplasmic end of helix TM7 and in helix H8.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

26 November 2018

Structure of rhodopsin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Structural features and light-dependent changes in the cytoplasmic interhelical E-F loop region of rhodopsin: a site-directed spin-labeling study

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1304048

Movement of retinal along the visual transduction path

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

Modelling alpha-helical transmembrane domains

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

The prediction and orientation of α-helices from sequence alignments: the combined use of environment-dependent substitution tables, Fourier transform methods and helix capping rules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

Hydrophobic moments and protein structure

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

PROCHECK: a program to check the stereochemical quality of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

Specific tryptophan UV-absorbance changes are probes of the transition of rhodopsin to its active state

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

DREIDING: a generic force field for molecular simulations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

Three-state and two-state models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974256-3

10.1016/S0006-3495(04)74256-3

7 January 2021

Identifiers

DOI

1 reference

19 September 2017

1 reference

19 September 2017

PubMed publication ID

15041637

1 reference