Arieh Warshel
Nobel Laureate, 2013 Chemistry Distinguished Professor of Chemistry and Biology at the University of Southern California (USA)
Nobel Laureate, 2013 Chemistry Distinguished Professor of Chemistry and Biology at the University of Southern California (USA)
MEDIATE project put at your disposal the VIRAL PROTEINS with the higher pharmaceutical interest and the BINDING SITES identified with our method recently published in the International Journal of Molecular Sciences. (for more details )
This novel strategy for pocket mapping, based on the combination of pocket and docking searches is proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which will be very useful for your MEDIATE virtual screening campaign.
All compounds were converted to 3D and prepared with Schrödinger’s LigPrep tool (Schrödinger Release 2020-2: LigPrep, Schrödinger, LLC, New York, NY, 2020.). This process generated multiple states for stereoisomers, tautomers, ring conformations (1 stable ring conformer by default) and protonation states. The Schrödinger package Epik was used to assign tautomers and protonation states that would be dominant at a selected pH range (pH=7±1).
Ambiguous chiral centers were enumerated, allowing a maximum of 32 isomers to be produced from each input structure. Then, an energy minimization was performed with the OPLS3 force field ([Harder2016]). Duplicates among the libraries were removed.
