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001009524 0247_ $$2datacite_doi$$a10.34734/FZJ-2023-02854
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001009524 1001_ $$0P:(DE-Juel1)180693$$aRaghavan, Bharath$$b0$$eFirst author
001009524 245__ $$aDrug Design in the Exascale Era: A Perspective from Massively Parallel QM/MM Simulations
001009524 260__ $$aWashington, DC$$bAmerican Chemical Society$$c2023
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001009524 500__ $$aGrant name: DBA01838 Innovative high-performance computing applied to neurodegenerative diseasesOpen access publication
001009524 520__ $$aThe initial phases of drug discovery – in silico drug design – could benefit from first principle Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics (MD) simulations in explicit solvent, yet many applications are currently limited by the short time scales that this approach can cover. Developing scalable first principle QM/MM MD interfaces fully exploiting current exascale machines – so far an unmet and crucial goal – will help overcome this problem, opening the way to the study of the thermodynamics and kinetics of ligand binding to protein with first principle accuracy. Here, taking two relevant case studies involving the interactions of ligands with rather large enzymes, we showcase the use of our recently developed massively scalable Multiscale Modeling in Computational Chemistry (MiMiC) QM/MM framework (currently using DFT to describe the QM region) to investigate reactions and ligand binding in enzymes of pharmacological relevance. We also demonstrate for the first time strong scaling of MiMiC-QM/MM MD simulations with parallel efficiency of ∼70% up to >80,000 cores. Thus, among many others, the MiMiC interface represents a promising candidate toward exascale applications by combining machine learning with statistical mechanics based algorithms tailored for exascale supercomputers.
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001009524 7001_ $$0P:(DE-Juel1)181088$$aPaulikat, Mirko$$b1$$eFirst author
001009524 7001_ $$0P:(DE-Juel1)186082$$aAhmad, Katya$$b2
001009524 7001_ $$00000-0003-0071-601X$$aCallea, Lara$$b3
001009524 7001_ $$0P:(DE-Juel1)180791$$aRizzi, Andrea$$b4
001009524 7001_ $$0P:(DE-Juel1)146009$$aIppoliti, Emiliano$$b5
001009524 7001_ $$0P:(DE-Juel1)190906$$aMandelli, Davide$$b6$$eCorresponding author
001009524 7001_ $$00000-0003-3028-0368$$aBonati, Laura$$b7
001009524 7001_ $$0P:(DE-Juel1)167585$$aDe Vivo, Marco$$b8
001009524 7001_ $$0P:(DE-Juel1)145614$$aCarloni, Paolo$$b9$$eCorresponding author
001009524 773__ $$0PERI:(DE-600)1491237-5$$a10.1021/acs.jcim.3c00557$$gVol. 63, no. 12, p. 3647 - 3658$$n12$$p3647 - 3658$$tJournal of chemical information and modeling$$v63$$x0095-2338$$y2023
001009524 8564_ $$uhttps://juser.fz-juelich.de/record/1009524/files/acs.jcim.3c00557.pdf$$yOpenAccess
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