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HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR

preprint
submitted on 30.06.2020, 05:29 and posted on 01.07.2020, 07:45 by Francesca Ferrari, Maicol Bissaro, Simone Fabbian, Jessica de Almeida Roger, Stefano Mammi, Stefano Moro, Massimo Bellanda, Mattia Sturlese

In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments producing a total of 1200 independent fragment-protein recognition pathways. As far as we know, this represents the largest screening based on Molecular dynamics ever reported. Our simulations successfully detected the true binders in the library in a prospective study, showing a notable agreement with a state-of-art screening we performed by NMR on the same dataset.

Funding

STARS Grants program, University of Padova. Project: SUMD4FBDD

PRID-J program (DSF, University of Padova). ID: stur_sid17_01

grant P-DiSC #01BIRD2018-UNIPD from the University of Padova

History

Email Address of Submitting Author

mattia.sturlese@unipd.it

Institution

University of Padova

Country

Italy

ORCID For Submitting Author

0000-0003-3944-0313

Declaration of Conflict of Interest

none

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Read the published paper

in Journal of Enzyme Inhibition and Medicinal Chemistry

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