David Bednář

Molecular modeling and bioinformatics

Computer is our friend not enemy!

  • Mission: Development of user-friendly bioinformatics tools.
  • Vision: Improving usage of computer predictions in precision medicine.

Due to the immense complexity of cancer, personalized oncology progressively substitutes the traditional “one-size-fits-all” therapy showing the treatment is more effective and with fewer side effects. On the other hand, this state-of-the-art approach requires identification of the mutated genes and their thorough analysis, which can be time-consuming and costly. Bioinformatics tools and databases present a valuable source of data that can help the multidisciplinary boards evaluate the mutations and suggest the right treatment. Sequence- and structure-based bioinformatics analyses provide information on the effect of mutation on protein structure, stability, dynamics, and function. Together with a search in available databases, it can distinguish between natural polymorphism and harmful mutations.

SELECTED PUBLICATIONS
  • Stourac J, Vavra O, Kokkonen P, Filipovic J, Pinto G, Brezovsky J, Damborsky J, Bednar D. Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 2019 Jul 2;47(W1):W414-W422. DOI: 10.1093/nar/gkz378
  • Stourac J, Dubrava J, Musil M, Horackova J, Damborsky J, Mazurenko S, Bednar D. FireProtDB: database of manually curated protein stability data. Nucleic Acids Res. 2021 Jan 8;49(D1):D319-D324. DOI: 10.1093/nar/gkaa981
  • Planas-Iglesias J, Opaleny F, Ulbrich P, Stourac J, Sanusi Z, Pinto GP, Schenkmayerova A, Byska J, Damborsky J, Kozlikova B, Bednar D. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res. 2022 Apr 19;50(W1):W465–73. DOI: 10.1093/nar/gkac249
  • Musil M, Jezik A, Jankujova M, Stourac J, Galgonek J, Mustafa Eyrilmez S, Vondrasek J, Damborsky J, Bednar D. Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web. Comput Struct Biotechnol J. 2022 Nov 17;20:6512-6518. DOI: 10.1016/j.csbj.2022.11.031
  • Stourac J, Borko S, Khan RT, Pokorna P, Dobias A, Planas-Iglesias J, Mazurenko S, Pinto G, Szotkowska V, Sterba J, Slaby O, Damborsky J, Bednar D, PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning, Brief Bioinform, 2024, 25(1):bbad441. DOI: 10.1093/bib/bbad441
SPECIALIZED EXPERTISE AND TECHNOLOGY

Molecular modelling

Bioinformatics

Machine learning

COLLABORATION WITH LARGE RESEARCH INFRASTRUCTURES AND RESEARCH CENTRES

Czech National Infrastructure for Biological Data ELIXIR CZ

RECETOX Centre

Czech Clinical Research Infrastructure Network CZECRIN