Modelling Interactions in Biomolecules Using Methods of Quantum and Molecular Mechanics

Project Leader: David Řeha (

Project Assistant: Zeenat Zara (

Project Aim:
The study of interactions between large biomolecules (proteins) with ligands (drugs) and other related bimolecular processes by means of advanced computational methods, particularly quantum mechanics (QM), hybrid QM/MM methods, molecular dynamics (MD) simulations and molecular docking.

Short annotation:
Computational methods are important tools in study of biomolecules including their interactions with other molecules (pharmaceutical drugs) and bimolecular processes. Within our project we would like to focus on very accurate description of the active site of the proteins and their interactions with ligands, substrates or protein co-factors. Such a level of accuracy can be only achieved by methods of quantum mechanics (QM). Since QM calculations are computationally very demanding and the description of the large biomolecules by purely QM methods is very limiting, hybrid QM/MM methods would be employed. We would like to apply QM/MM methods for calculation of the binding energy of various ligands in proteins as well as classical MD simulations in order to study biologically relevant molecules.