Low inhibiting power of N...CO based peptidomimetic compounds against HIV protease: Insights from a hybrid QM/MM study
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Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...
A method based on molecular dynamics simulations which employ two distinct levels of theory is proposed and tested for the prediction of Gibbs free energies of solvation for non-ionic solutes in water. The method consists of two additive contributions: (i) ...
High-Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi-threading and distributed computing) used in all the natural sciences, including molecular bi ...
At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...
We derive and validate averaged solvent parameters for embedding potentials to be used in polarizable embedding quantum mechanics/molecular mechanics (QM/MM) molecular property calculations of solutes in organic solvents. The parameters are solvent-specifi ...
The computational method was used to explain the activity of zein-based colloidal nanoparticles at inter-face between water and oil phases. The alpha-zein/tannic acid colloidal nanoparticles (ZTPs) were made using three steps including dissolving alpha-zei ...
Atomistic simulations are a powerful complement to experimental probes for understanding the nanoscale processes associated with the effects of hydrogen (H) on plasticity and fracture that are the underlying causes of hydrogen embrittlement (HE). Current e ...
The temperature dependence of the femtosecond elastic second harmonic scattering (fs-ESHS) response of bulk light and heavy water and their electrolyte solutions is presented. We observe clear temperature dependent changes in the hydrogen (H)-bond network ...
Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quant ...
The intrinsic structures of biomolecules in the gas phase may not reflect their native solution geometries. Microsolvation of the molecules bridges the two environments, enabling a tracking of molecular structural changes upon hydration at the atomistic le ...
