The thesis first focuses on existing empirical methods for partial atomic charge calculation and their implementation in the Atomic Charge Calculator II web server, with some of the methods being implemented there for the first time ever. The next part of the thesis introduces the SQE+qp, an empirical method for partial atomic charge calculation with cutting-edge quality results for proteins. This advantage of the SQE+qp method is utilised in the αCharges web server presented in the final part of the thesis. Charges provides the ability to automatically protonate any protein in the AlphaFold DB and compute the protein's partial atomic charges that are useful for further research.
Congratulations, Ondřej!
PDBCharges, a tool providing partial atomic charges for protein structures from the Protein Data Bank, was published in the journal Nucleic Acids Research.
