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Methods

Published on 25 January 2019


Structure prediction
We mainly use the program MODELLER to make protein structure predictions by homology.

Molecular Mechanics and Dynamics (MM/MD)

Quantum chemistry, quantum mechanics (QM)

QM/MM (Quantum Mechanics/Molecular Mechanics) applied to bio-inorganic chemistry
Yohann Moreau

In order to understand the properties and reactivity of metallo-enzymes and related systems, we make use of quantum-based methods, such as Density Functional Theory. This approach allows one to get information on the electronic properties and study the related reactivity. Due to the computational cost of such methods, only model systems can be studied by QM only.
The reactivity of metalloenzymes, can be dramatically influenced by their whole structure. Hence, it is of crucial interest to take it into account. Since it is impossible to describe the whole structure, we make use of a multiscale approach in which the active site is describe by the mean of QM while the environment classically (molecular mechanics). The QM/MM approach allows to include the environmental effects (polarization, steric effects) at a reasonable cost.



X-Ray absorption and fluorescence
Giulia Veronesi