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Message boards : News : New paper 1/2: PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulation

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Toni
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Message 55110 - Posted: 24 Jul 2020 | 16:23:08 UTC
Last modified: 24 Jul 2020 | 16:30:23 UTC

Two recent papers which came out with results from GPUGRID.

First,


PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations
Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, and Gianni De Fabritiis
Journal of Chemical Information and Modeling 2020 60 (4), 2314-2324
DOI: 10.1021/acs.jcim.9b01209


In this paper (and the corresponding live system) GPUGRID's computations are used to power a search for elusive (transient) pockets which may become drug targets.

Thanks for the contributions!




Cryptic pockets are protein cavities that remain hidden in resolved apo structures and generally require the presence of a co-crystallized ligand to become visible. Finding new cryptic pockets is crucial for structure-based drug discovery to identify new ways of modulating protein activity and thus expand the druggable space. We present here a new method and associated web application leveraging mixed-solvent molecular dynamics (MD) simulations using benzene as a hydrophobic probe to detect cryptic pockets. Our all-atom MD-based workflow was systematically tested on 18 different systems and 5 additional kinases and represents the largest validation study of this kind. CrypticScout identifies benzene probe binding hotspots on a protein surface by mapping probe occupancy, residence time, and the benzene occupancy reweighed by the residence time. The method is presented to the scientific community in a web application available via www.playmolecule.org using a distributed computing infrastructure to perform the simulations.



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[CSF] Thomas H.V. Dupont
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Message 55112 - Posted: 24 Jul 2020 | 16:30:44 UTC

Nice!
Thanks so much Toni!
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[CSF] Thomas H.V. Dupont
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[CSF] Thomas H.V. Dupont
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Message 55114 - Posted: 24 Jul 2020 | 16:41:51 UTC

https://pubs.acs.org/doi/10.1021/acs.jcim.9b01209
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[CSF] Thomas H.V. Dupont
Founder of the team CRUNCHERS SANS FRONTIERES
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Message 55119 - Posted: 25 Jul 2020 | 10:47:47 UTC

A shame we can't read it.

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Message 55120 - Posted: 25 Jul 2020 | 14:57:53 UTC - in response to Message 55110.

It looks suspiciously relevant to COVID-19 to me, though of broader applicability as well. Good work, no doubt.

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Message 55125 - Posted: 26 Jul 2020 | 5:26:16 UTC
Last modified: 26 Jul 2020 | 6:01:59 UTC

User names added to the list of most contributing users.
Any errors please correct as required.
Some of the users in the list have not contributed since 2018, so paper(s) appear to draw from older work units. (to be expected)

User Rank Credits 101936 1 4639746 Rion Family 14310 2 4450949 Retvari Zoltan 483287 3 3535477 grcpool.com 103037 4 2362054 Zalster 500240 5 1986559 grcpool.com-2 25378 6 1969784 Stoneageman 504924 7 1945416 grcpool.com-3 100499 8 1834758 jjch 73475 9 1796967 Viktor Svantner 125700 10 1755579 Erich56 126468 11 1651313 Gunde 306281 12 1638950 PappaLitto 62100 13 1542475 vanos0512 21233 14 1536750 James C. Owens 535400 15 1364758 davidBAM 13127 16 1161000 Betting Slip 509733 17 1035000 xii5ku 28899 18 973950 Bob Deller 543022 19 971404 Science United 89682 20 946350 flashawk

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Message boards : News : New paper 1/2: PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulation