Research Focus

Our laboratory is multidisciplinary and comprises three sections, devoted to: development of bioinformatic methods and databases, application of computational tools to study particular macromolecules, and experimental research on protein-nucleic acid interactions. In the past, our group has developed software tools for protein structure prediction, including the GeneSilico [1] meta-server for protein 3D structure prediction, and TOOLKIT [2], a set of online tools for generation, validation and experimental probing of structural models. On the RNA side, we developed the first database of RNA modification pathways MODOMICS [3]. Currently we are involved in modeling studies on a number of proteins important for splicing regulation, and we are developing new tools for structure prediction of RNA and protein-RNA complexes.

Publications

1. Palfi, Z., Jaé, N., Preusser, C., Kaminska, K.H., Bujnicki, J.M., Lee, J.H., Günzl, A., Kambach, C., Urlaub, H., Bindereif, A. (2009). SMN-assisted assembly of snRNP-specific Sm cores in trypanosomes. Genes and Development 23(14), 1650-64.
2. Pietal M, Tuszynska I, Bujnicki JM (2007). PROTMAP2D: visualization, comparison, and analysis of 2D maps of protein structure.. Bioinformatics 23(11), 1429-30.
3. Bujnicki, J.M. (2006). Protein-structure prediction by recombination of fragments. Chembiochem 7, 19-27.
4. Dunin-Horkawicz, S., Czerwoniec, A., Gajda, M.J., Feder, M., Grosjean, H. and Bujnicki, J.M. (2006). MODOMICS: a database of RNA modification pathways. Nucleic Acids Research 34, D145-149.
5. Kosinski, J., Cymerman, I.A., Feder, M., Kurowski, M.A., Sasin, J.M. and Bujnicki, J.M. (2003). A "FRankenstein's monster" approach to comparative modeling: merging the finest fragments of Fold-Recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 53 Suppl 6, 369-379.
6. Kurowski, M.A. and Bujnicki, J.M. (2003). GeneSilico protein structure prediction meta-server. Nucleic Acids Research 31, 3305-3307.

Key lab techniques: Algorithms for protein and RNA structure prediction, modeling of protein-protein and protein-nucleic acid complexes, protein and RNA biochemistry.

Key lab reagents: Protein and RNA sequences and structures, Python programming language.

Interest in alternative splicing: I am fascinated by the complexity of the spliceosome. Currently there is no single technique with which to determine its detailed structure and dynamics and mechanism of function. I believe structural bioinformatics will be the key approach to integrate the available data for different forms and parts of the spliceosome, to provide useful working models.

Lab contact: Olga Babcka: ola@genesilico.pl [4]

Lab website: http://genesilico.pl [5]