Everything about your study
in one of the most beautiful cities in the world

Bioinformatics/software engineering

Research at Charles University

Research project: Structural bioinformatics

Our research in bioinformatics focuses on the development of software tools applicable mainly in the domain of structural bioinformatics and visualization. These include tools for protein binding site detection, with the application in computational drug discovery, or tools for visualization of the structure of macromolecules. All our methods are implemented as software solutions used by thousands of users all over the world.

Team leader & members

Small interdisciplinary team core of which consists of PIs, postdocs and doctoral students; we also involve graduate and undergraduate students in individual subprojects.

Publications

  • Blake A. S., Hoksza D., Nawrocki E., Ribas C. E., Madeira F., Cannone J. J., Gutell R., Maddala A., Meade C. D., Williams L. D., Petrov A. S., Chan P. P., Lowe T. M., Finn R. D., Petrov A. I. (2021) R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nature Communications 12 (1): 1-12
  • RNAcentral Consoritum, Hoksza. D. (2021) RNAcentral 2021: secondary structure integration, improved sequence search, and new member databases. Nucleic Acids Research 49 (D1): D212-D220
  • Iqbal, S., Pérez-Palma, E., Jespersen, J. B., May, P., Hoksza, D., Heyne, H. O., … & Lal, D.. (2020) Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants. Proceedings of the National Academy of Sciences 117 (45): 28201-28211
  • PDBe-KB consortium (2020) PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Research 48 (D1): D344–D353
  • Krivák, R., & Hoksza, D. (2018) P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. Journal of cheminformatics 10(1)

Contact

Charles University
Faculty of Mathematics and Physics
Doc. Mgr. Martin Nečaský, Ph.D.
E: martin.necasky@matfyz.cuni.cz

More information

https://www.ksi.mff.cuni.cz

#benewmember
#ScienceAndResearch
#FacultyOfMathematicsAndPhysics

Univerzita Karlova v Praze