In collaboration of the National Centre for Biomolecular Research at the Faculty of Science, Masaryk University, and the CESNET Development Fund, a project led by Ondřej Schindler, Tomáš Svoboda, Gabriela Bučeková and Lukáš Bohuš was carried out, focusing on the optimisation of protein structures predicted by AI. As part of the project, a tool for correcting non-physically placed atoms, PROPTIMUS PRIME, and a tool for the rapid optimisation of proteins with restricted α-carbons, PROPTIMUS RAPHAN, were developed. These tools have been made available to the scientific community via the PROPTIMUS LIVE web application.
The results of this project were published in the journals Journal of Cheminformatics and Nucleic Acids Research. The publications include the articles titled Analysis of structural errors in the AlphaFold DB v4 and v6, Per-residue optimisation of protein structures: a rapid alternative to local optimisation with constrained alpha carbons and PROPTIMUS LIVE: local constrained α-carbon optimisation of proteins.
On 3rd September, our colleague Gabriela Bučeková successfully defended her dissertation thesis at the Faculty of Science, Masaryk University. Her thesis topic is "Bioinformatics analysis of protein properties".
Atomic Charge Calculator III, developed by the Structural Bioinformatics research group, was published in the NAR Web Server Issue 2026 and featured on the issue cover.
