Award for Excellence in Doctoral Studies
On 7 November 2024, Ondřej Schindler, a member of the Structural Bioinformatics research group, was awarded the prestigious Vice-Rector's Award for Excellence in Doctoral Studies.
PDBCharges was published in an article
The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230,000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for the quick calculation of partial atomic charges for protein structures from PDB.
The charges are computed by the semiempirical quantum mechanical methods GFN1-xTB and reproduce the PBE0/TZVP/CM5 charges. Before the computation of the charges, hydrogens are added to the structure by Hydride and MoleculeKit at pH 7.2. The positions of the added hydrogens are also optimised using the GFN-FF force field.
PDBCharges was recently published in the Web Server issue of the Nucleic Acids Research journal. Its article is titled PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.
PDBCharges is available at https://pdbcharges.biodata.ceitec.cz/.
