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

Nature chemistry, 2014-01, Vol.6 (1), p.15-21 [Peer Reviewed Journal]

Copyright Nature Publishing Group Jan 2014 ;ISSN: 1755-4330 ;EISSN: 1755-4349 ;DOI: 10.1038/nchem.1821 ;PMID: 24345941

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  • Title:
    Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
  • Author: Kohlhoff, Kai J ; Shukla, Diwakar ; Lawrenz, Morgan ; Bowman, Gregory R ; Konerding, David E ; Belov, Dan ; Altman, Russ B ; Pande, Vijay S
  • Subjects: Internet ; Ligands ; Markov Chains ; Receptors, G-Protein-Coupled - metabolism
  • Is Part Of: Nature chemistry, 2014-01, Vol.6 (1), p.15-21
  • Description: Simulations can provide tremendous insight into the atomistic details of biological mechanisms, but micro- to millisecond timescales are historically only accessible on dedicated supercomputers. We demonstrate that cloud computing is a viable alternative that brings long-timescale processes within reach of a broader community. We used Google's Exacycle cloud-computing platform to simulate two milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2AR. Markov state models aggregate independent simulations into a single statistical model that is validated by previous computational and experimental results. Moreover, our models provide an atomistic description of the activation of a G-protein-coupled receptor and reveal multiple activation pathways. Agonists and inverse agonists interact differentially with these pathways, with profound implications for drug design.
  • Publisher: England: Nature Publishing Group
  • Language: English
  • Identifier: ISSN: 1755-4330
    EISSN: 1755-4349
    DOI: 10.1038/nchem.1821
    PMID: 24345941
  • Source: MEDLINE
    ProQuest Central
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