- Development of tools for modeling and analysis of RNA and RNP 3D structures. We develop software for modeling of RNA structures and for prediction of RNA-ligand interactions. Examples include ModeRNA (for comparative modeling of RNA 3D structures), SimRNA (for folding simulations of RNA), DARS-RNP (for RNA-protein docking), and LigandRNA (for RNA-ligand docking).
- Development of tools for protein structure prediction. We develop software for protein structure prediction from sequence. The pipeline of methods developed in our laboratory includes the fold recognition metaserver, modeling tools, and model quality assessment tools and is available via the GeneSilico TOOLKIT. The most recent addition is QA-RecombineIt, a method for model assembly from fragments combined with model quality assessment.
- Development of databases of nucleic acid metabolism. We developed the MODOMICS database of systems biology of posttrascriptional RNA modification and REPAIRtoire, a database of DNA repair pathways.
- Characterization of novel enzymes involved in RNA metabolism. We predict (using bioinformatics) and characterize experimentally novel enzymes, in particular RNA methyltransferases and RNases.
- Protein engineering. We use computational and experimental techniques to (re)design and create experimentally enzymes with new functions, e.g. restriction enzymes with new substrate speificities. Our recent success is the development of eRNases: restriction enzymes that cleave RNA sequence-specifically.
- Discovery of candidates for new drug leads. We use high-throughput virtual screening in combination with experimental analyses to identify candidates for inhibitors of enzymes from human pathogens (bacteria and viruses).
These research projects are currently funded by:
ERC (European Research Council - EU) - ERC-StG grant
FNP (Foundation for Polish Science - Poland) - TEAM grant
NCN (National Science Centre - Poland) - MAESTRO grant to J.Bujnicki and a number of various grants to Bujnicki lab members
MNiSW (Ministry of Science and Higher Education - Poland) - research, special, SPUB, and PhD grants
6&7 FP (Framework Programme - EU) - EURASNET Network of Excellence