List

* Using idle computers to stretch simulations, Nature Methods, 11, 129 (2014) doi:10.1038/nmeth.2821

G protein–coupled receptors (GPCRs) control important signaling pathways in the body and are the targets of over one-third of medical drugs. Predicting how GPCRs convert between active and inactive forms can provide insights into ligand binding and suggest new modes of activation, but detailed molecular dynamics simulations require modeling thousands of atoms and are feasible only on supercomputers. Kohlhoff et al. now take advantage of excess cloud computing power at Google to carry out an atomic-scale simulation of the GPCR β2-adrenergic receptor, which is involved in obesity, diabetes and asthma. They use idle time on servers with Google Exacycle and then use Markov state modeling to compile shorter simulations into a two-millisecond-long model, revealing a number of parallel conformational pathways and breaking the previous simulation length record by an order of magnitude.

* Cloud computing gives insights into activation, Charlotte Harrison, Nature Reviews Drug Discovery, 13, 104, (2014) doi:10.1038/nrd4247

Molecular dynamics simulations can reveal important information about receptor activation, but often require specialist hardware. To overcome this limitation, Kohlhoff et al. used cloud computing to investigate the mechanism that underlies β2-adrenergic receptor activation. Tens of thousands of independent simulations were run on Google Exacycle, which were then integrated into a single statistical model. This captured multiple previously unidentified discrete conformational states of the receptor, which were linked to different activation pathways; agonists and inverse agonists interacted differentially with these pathways.

  Posts

December 7th, 2016

Group Picture time in our lab!

http://www.shuklagroup.org/wp-content/uploads/2016/12/GroupPhotoDec2016.mp4
September 25th, 2016

Summer Intern Nikhil Sethia’s (IIT Delhi) Post on his experiences in Shukla Group.

Hello readers. I am Nikhil Sethia, a junior undergraduate majoring in Chemical Engineering at Indian Institute of Technology Delhi, India. […]

September 25th, 2016

Prof. Shukla’s talk on “Molecular Models of Nitrate Transport in Plants” at Plants in silico Symposium, 2016.

September 25th, 2016

Talk by Graduate Student Alex Moffett at 2016 Blue Waters Symposium at Sunriver Resort, Oregon.

December 21st, 2015

Research Talk by Prof. Shukla (CSE Seminar Series, Fall 2015)

October 22nd, 2015

Teaching kids about protein structure and function at Booker T. Washington STEM Academy

Our group recently visited Booker T. Washington STEM Academy in Champaign, Illinois to teach underrepresented fourth and fifth grade boys […]

July 20th, 2015

Research talk by Diwakar (Blue Waters Symposium, Jun 2015)

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July 17th, 2015

Plants in silico: a multi-scale modeling platform

Tools capable of predicting emergent crop phenotypes in response to climate change are needed to evaluate risk to food security […]

July 13th, 2015

Girls’ Adventures in Mathematics, Engineering & Sciences (GAMES) camp, 2015.

Shukla Group organized several activities related to the Computational Investigations of Protein Structure & function as part of the GAMES […]

May 30th, 2014

Central themes of our research group

Modern computational chemistry approaches have been increasingly used for obtaining molecular understanding of biological systems and the design of novel […]

March 11th, 2014

Recent paper on the key cellular signaling proteins in Cancer highlighted in several news articles

For more details read the news item below or find all the new coverage and reviews on Altmetric site here. […]

February 1st, 2014

GPCR activation work highlighted in Nature Methods and Nature Reviews Drug Discovery journals.

* Using idle computers to stretch simulations, Nature Methods, 11, 129 (2014) doi:10.1038/nmeth.2821 G protein–coupled receptors (GPCRs) control important signaling […]

January 1st, 2014

Nature Chemistry article highlighted across scientific news blogs.

Stanford News reports “Stanford and Google team up to simulate key drug receptor” Chemical & Engineering News reports “Receptor Simulation […]