Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study
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We present QMMMW, a new program aimed at performing Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics. The package operates as a wrapper that patches PWscf code included in the QUANTUM ESPRESSO distribution and LAMMPS Molecular Dynamics Simu ...
CONSPECTUS: Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by ...
Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, b ...
Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes ob served upon electron abstraction of aqueous iodide, which reflects the transit ...
Metallo-beta-lactamases (M beta Ls) are Zn(II)-based bacterial enzymes that hydrolyze beta-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from point to either two zinc ...
Polarizable quantum mechanical (QM)/molecular mechanics (MM)-embedding methods are currently among the most promising methods for computationally feasible, yet reliable, production calculations of localized excitations and molecular response properties of ...
The overarching objective of this thesis is extending and adapting the set of computational tools available for describing molecular precursors of organic semiconductors. The research presented within develops adhering to three principle goals: (1) provide ...
Myoglobin modulates the binding of diatomic molecules to its heme group via hydrogen-bonding and steric interactions with neighboring residues, and is an important benchmark for computational studies of biomolecules. We have performed calculations on the h ...
We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers ...
The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins ...
