Laboratory of Computational Chemistry


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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

MutH active site

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, glycohydrolases and acetylcholine esterase 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.

Coarse Grained Simulations

Virus capsid

We study cellular uptake of nanoparticles and virus capsids. These processes are crucial for drug delivery, toxicity, and nanomedicine. We investigate conditions of passive endocytosis of ligand-coated particles of various sizes, shapes, and coverage across a zero-tension, receptor-rich, phospholipid membrane. We also develop new coarse grained models for studying self-assembly of rod like molecules (peptides, carbon nanotubes, etc.). Using these models we determine crucial parameters that lead to different aggregated morphologies including barrels, fibrils, ribbons, bilayers and other oligomers.

Chemoinformatics and 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.