Cheminformatics and Interoperability of chemical and biological databases

We are working on small-molecule databases and search infrastructure for the ELIXIR project, the research concerns molecular fingerprinting, high-performance queries and maintenance of IOCB IDSM database tools. Recently we have started to contribute to machine-assisted processing, analysis and visualization of flow cytometry data.

Protein - DNA Interactions.  Bioinformatics on biomolecular complexes

We are interested in isolating minimal structural protein motifs possessing DNA-binding activity which could act as templates for the development of sequence-specific DNA-binding peptides. To this end, we combine bioinformatical (database mining), computational (simulations of protein--DNA complexes), and experimental (calorimetric, thermophoretic) approaches. Specialized branch of bioinformatical studies involves the analysis of DNA geometry in complexes with proteins.

Coevolution of Protein Domains and Design of Multi-Domain Proteins

Allosteric modulation of a protein domain function is one of the most intriguing concepts in molecular biology nowadays . Small tandem domains represent ideal candidates to decipher mechanism of binding specificity via adjacent domains synergy in multi-domain protein context by means of structural, computational and biophysical methods. Ultimate goal of this project is to understand the phenomenon of allostery brought by adjacent domain together with folding, structure, dynamics and binding properties of the fusion proteins. Our model systems contain PDZ3 domain in various 2 domains fusion constructs and our aim is to describe the mechanism in which PDZ3 specificity is controlled by a character, position and size of the attached domain. This can make possible to contribute to the domains coevolution phenomenon.