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Articles by Fréderic Célerse
Capturing Dichotomic Solvent Behavior in Solute–Solvent Reactions with Neural Network Potentials
1. Introduction Click to copy section linkSection link copied! Often, in synthetic chemistry, the role of solvents is noninnocent. Whereas chemically inert nonpolar solvents influence reactivity predominantly through weak noncovalent solute–solvent interactions, protic solvents have the potential to react directly with the solute. Reactivity of this type has been harnessed to create new reactions.
AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1
Abstract Long oligomer sequences, rich in guanine and cytosine, such as c-kit1 and the HIV-1 LTR-III sequence, are prevalent in oncogenes and retroviruses and play crucial roles in cancer. Understanding the conformational dynamics of such guanine quadruplexes and identifying druggable regions are therefore essential for developing new inhibition strategies.
AMOEBA Polarizable Molecular Dynamics Simulations of Guanine Quadruplexes: from the c-Kit Proto-oncogene to HIV-1
Abstract We report extensive Molecular Dynamics (MD) simulations using the AMOEBA polarizable force field on two guanine quadruplex-forming oligonucleotides. The first belongs to the c-kit1 proto-oncogene, and the second to the LTR-III sequence of the HIV-1 retrovirus. The simulations were powered by a non-supervised adaptive sampling strategy, enabling a cumulated simulation time of 7.5 µs for c-kit1.
From Organic Fragments to Photoswitchable Catalysts: The OFF-ON Structural Repository for Transferable Kernel-Based Potentials
Special Issue Published as part of Journal of Chemical Information and Modeling virtual special issue “Modeling Reactions from Chemical Theories to Machine Learning”. Machine learning (ML)-based potentials have served as efficient ab initio surrogates for molecular dynamics (MD) simulations, enabling statistically converged free energy surfaces (FESs) to be computed at DFT-level accuracy with significantly reduced computational cost.
Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface
In the context of COVID-19 drug discovery, both structural and nonstructural proteins are considered as promising targets for the development of antiviral agents against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).(1) Specifically, SARS-CoV-2 Mpro plays a pivotal role in controlling viral replication and transcription through proteolytic processing of viral poly proteins.(2) Many studies on inhibitor ligands are based on active site pocket targeting.
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