Computational Chemistry - Jaroslav Koča
Computational Chemistry - Jaroslav Koča


Prof. Jaroslav Koča Prof. Jaroslav Koča
Research Group Leader Senior
Petr Kulhánek, Ph.D. Petr Kulhánek, Ph.D.
Senior Staff Scientist

Research areas

  • Structure and dynamics of proteins, nucleic acids, saccharides, and their complexes in relationship to their biological function
  • Mechanistic studies on enzymatic reactions
  • Chemoinformatics and structural bioinformatics
  • Structure and dynamics of supramolecular complexes

Main objectives

  • To study the therapeutical and bioanalytical aspects of recognition and adhesion phenomena in host-pathogen interactions
  • To develop new methodologies for investigating the structure, interactions, and dynamics of biomolecules
  • Development of new tools for structural bioinformatics and chemoinformatics

Content of research

The group uses methods of computational chemistry, chemoinformatics and structural bioinformatics to study  proteins, nucleic acids and their complexes. It works on development of computational approaches for structural and functional studies of biomolecules.

Computational chemistry helps to interpret experimental observations or to get a new information about systems where experimental approaches are not applicable or difficult to apply. It is widely employed in, for example, design and studies on new molecules with a possible biological impact.

Chemoinformatics and Structural Bioinformatics

Nowadays, a large amount of information about biomolecules (i.e. sequence of DNA, structure of proteins) and about small molecules (drug-like molecules, ligands, etc.) is available. Main goal of bioinformatics and chemoinformatics research is a processing of these data, which can provide information very useful in pharmacy, medicine, biotechnology etc. Our laboratory is focusing on advanced analyses of protein 3D structures, processing data from next generation sequencing and predicting of physico-chemical properties of organic molecules.

Structure and Dynamics of Biomolecules

We use a wide spectrum of state-of-the-art computational techniques to study structure and dynamics of short peptides, proteins, enzymes, and short nucleic fragments. Our main attempt is to understand how these biomolecules are assembled in space and how their structure is related to their function. We use a molecular docking to predict unknown structures of complexes between proteins and small molecules. Interactions are studied by several approaches ranging from very precise quantum chemical calculations to methods employing molecular mechanics.

Enzymatic Reactions

The understanding of reaction mechanisms is essential step in rational design of enzyme inhibitors that might act as drugs. We employ hybrid quantum mechanics (QM) / molecular mechanics (MM) approach to find the most probable reaction pathways. Various techniques to explore complicated potential (free) energy surfaces are used. They range from single/double coordinate energy scans to advanced techniques employing free energy calculations and Car-Parrinello dynamics. Developed techniques are used to study nucleases, glycotransferases and glycohydrolase enzymes.

Supramolecular Chemistry

Structure, stability and reactivity of supramolecular systems are studied by molecular modeling techniques, including both quantum and molecular mechanics approaches. Key molecules in our projects are glycoluril oligomers such as cucurbit[n]urils and bambus[n]urils. We study their interactions with various organic and inorganic guests. Our main attention is focused on reliable description of forces leading to complex assembly, which might be used in rational host modifications providing desired properties.

Software development

Mole Sum




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