Laboratory of Computational Chemistry

Head: RNDr. Petr Kulhánek, Ph.D.

About Us

Our research group uses computational approaches to study chemical and biochemical problems. We combine chemistry, physics, mathematics, molecular modelling and information technology to investigate the properties of supramolecular and biomolecular systems. We use state-of-the-art methods for quantum mechanical calculations, docking, molecular dynamics, free energy calculations, chemoinformatics and bioinformatic analyses. In addition, we contribute new simulation protocols and methods using high-performance programming languages, especially Fortran and C/C++.

RNDr. Petr Kulhánek, Ph.D.



Ing. Tomáš Trnka, Ph.D.

Deputy Head of Group


Research Topics

Our current research is focused on three areas: enzymatic reaction mechanisms, mechanical properties of biomolecules, and binding affinities in supramolecular chemistry.

We study the reaction mechanisms of bacterial glycosyltransferases with unknown or incomplete structural information. Using computational approaches, we complement experimental knowledge with atomistic details of the reaction mechanisms. The findings are crucial for the design of next-generation antibiotics based on inhibitors of the studied enzymes.

We also study the mechanical properties of biomolecules essential in key biomolecular processes. Specifically, we study how the properties of DNA change in the presence of non-canonical base pairing. This knowledge is important to understand the repair mechanisms targeting DNA damage introduced during replication.

Finally, we investigate the binding free energies associated with the formation of supramolecular complexes. Our methodology provides enthalpy, entropy, and free energy calculations from a single simulation. Their knowledge is crucial for understanding the effect of enthalpy/entropy compensation (EEC). This effect greatly complicates the rational design of new drugs.

What we offer

Beyond working on interesting problems in chemistry and structural biology, we teach students how to work in a Linux environment. You will gain practical skills in scripting languages, including Bash, Awk, Gnuplot, and Python. For those keen on expanding their knowledge, we offer our experience in advanced programming languages like C/C++ and Fortran. You will also gain experience using advanced computational tools such as AMBER for biomolecular simulations, Orca and Gaussian for quantum chemical calculations, AutoDock, Amsterdam Modeling Suite and many others. We will teach you how to organize data and perform challenging simulations in the MetaCentrum environment, a grid supercomputing centre in the Czech Republic.

Our students can work on projects remotely. We provide easy-to-use tools for remote desktop access from any web browser. You can work from study rooms or your computers running any operating system.


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