Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways (Q37582165)

21 August 2017

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways (English)

1 reference

G protein-coupled receptor

21 August 2017

0 references

Google

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corrigendum / erratum

Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

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7

Russ B Altman

1 reference

21 August 2017

8

Vijay S Pande

1 reference

21 August 2017

Kai J Kohlhoff

1

1 reference

21 August 2017

Diwakar Shukla

2

1 reference

21 August 2017

Morgan Lawrenz

3

1 reference

21 August 2017

Gregory R Bowman

4

1 reference

21 August 2017

David E Konerding

5

1 reference

21 August 2017

Dan Belov

6

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21 August 2017

15 December 2013

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21 August 2017

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21 August 2017

6

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21 August 2017

1

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21 August 2017

15-21

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

21 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

The dynamic process of β(2)-adrenergic receptor activation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Efficacy of the β₂-adrenergic receptor is determined by conformational equilibrium in the transmembrane region

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

ZINC: a free tool to discover chemistry for biology

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Surflex-Dock: Docking benchmarks and real-world application

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Ligand and decoy sets for docking to G protein-coupled receptors

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Activation mechanism of the β2-adrenergic receptor

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Crystal structure of the β2 adrenergic receptor-Gs protein complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Structure and function of an irreversible agonist-β(2) adrenoceptor complex

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Structure of a nanobody-stabilized active state of the β(2) adrenoceptor

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Conformer generation with OMEGA: algorithm and validation using high quality structures from the Protein Databank and Cambridge Structural Database

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Reactive flux and folding pathways in network models of coarse-grained protein dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Using generalized ensemble simulations and Markov state models to identify conformational states

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Transition-path theory and path-finding algorithms for the study of rare events

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Transition networks for modeling the kinetics of conformational change in macromolecules

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

COMPUTING: Screen Savers of the World Unite!

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

OPM: orientations of proteins in membranes database

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Virtual screening of chemical libraries

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Discovery of a novel binding trench in HIV integrase.

23 August 2017

1 reference

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VMD: visual molecular dynamics

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

To milliseconds and beyond: challenges in the simulation of protein folding

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Structure-based drug screening for G-protein-coupled receptors

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

EMMA: A Software Package for Markov Model Building and Analysis.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Activation of the beta 2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

The forgotten serine. A critical role for Ser-2035.42 in ligand binding to and activation of the beta 2-adrenergic receptor.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

The effect of pH on beta(2) adrenoceptor function. Evidence for protonation-dependent activation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3923464

Anton, a special-purpose machine for molecular dynamics simulation

1 September 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCHEM.1821

Conserved aspartic acid residues 79 and 113 of the beta-adrenergic receptor have different roles in receptor function

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24345941

12 December 2020

inferred from PubMed ID database lookup

FlumeJava: Easy, Efficient Data-Parallel Pipelines

1 reference

https://api.crossref.org/works/10.1038%2FNCHEM.1821

7 January 2021

inferred from DOI database lookup

MapReduce: Simplified Data Processing on Large Clusters

1 reference

https://api.crossref.org/works/10.1038%2FNCHEM.1821

7 January 2021

inferred from DOI database lookup

Bigtable: A Distributed Storage System for Structured Data

1 reference

https://api.crossref.org/works/10.1038%2FNCHEM.1821

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1038/NCHEM.1821

1 reference

21 August 2017

1 reference

21 August 2017

PubMed publication ID

24345941

1 reference