My lab is involved in plenty of interesting projects. Briefly, we study structure - function relationships of cytokines, e.g. Interferon gamma, Interleukin 24, Interleukin 26, study protein/DNA interactions in a system of bacterial non-coding REP sequences (Repetitive palindromic sequences) associated with so called RAYT transposase, and work on bioinformatic analysis of nucleic acid structures. More can be seen at the web pages of the laboratory. Our published works are here.

My second major responsibility is to coordinate the research program of Structural biology and protein engineering at the BIOCEV center (the Biotechnology and Biomedicine Centre of the Czech Academy of Sciences and Charles University). The project has been funded by the European Regional Development Fund.

Understanding mechanisms of molecular recognition is the Holy Grail of structural biology, at least as I understand goals of structural biology. To get closer to reaching this goal, I study structure, dynamics, and solvation of nucleic acids, and proteins.

Both DNA and RNA dinucleotides form a limited set of conformers. Some, as BI ("b-one") or "canonical A" are abundant and form the scaffold of DNA double helices (BI) or RNA complex architectures (AI). Other conformers are rare but occur at structurally and functionally critical points. Especially RNA molecules with their complicated 3D folds employ a repertoire of unusual but structurally well defined conformers. More can be found at our website dnatco.org and in our papers for definition of the structural classes and for an application.

Solvation, water activity, presence and concentration of ions, especially cations, are important for structural integrity of nucleic acids and therefore for their function. Since the early nineties, I have been involved in research of structural aspects of DNA solvation in the lab of Prof. Helen Berman at Rutgers University, NJ and later in Prague. Recently, Lada Biedermannová, Jiří Černý & I determined positions and importance (intensities) of hydration sites around amino acids in proteins watAA and now with Ela Nekardová we work on the same task for DNA dinucleotide conformers. These results have general validity because they have been drawn solely from experimental crystal data with no bias of any "theoretical" model.

I have been privileged to work with Professor Helen Berman at Rutgers University on development of two important databases of molecular structures, first the Nucleic Acid Database, NDB and later on the Protein Data Bank, PDB. Between the years 1998 and 2008 I was a member of the team maintaining the NDB and I annotated structures deposited to the PDB. In the years 2000-2008, after I returned to Prague, structures deposited at Rutgers were annotated in Prague. What is annotation of biomolecular structures? If you really want to know, you can read a paper where three annotators explain what is involved before a molecular structure can be loaded into the PDB: Burkhardt, Schneider, Ory, 2006.