PDBCharges: Quantum-mechanical partial atomic charges for PDB structures
| Authors | |
|---|---|
| Year of publication | 2025 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | The PDB is the largest database of experimentally determined protein structures, containing more than 230 thousands of structures. A clue to the chemical reactivity of proteins is the electron density distribution, which is usually approximated by partial atomic charges. Due to the size and high variability of the structures stored in the PDB database, 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 calculated by the recent semiempirical quantum mechanical method GFN1-xTB reproducing PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualised via the powerful Mol* viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz/ with no login requirement. |
| Related projects: |