Journal Article Ppublish 1 citation
PubMed: 40347106 DOI: 10.1093/nar/gkaf401
PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.
Nucleic Acids Res 53(W1):W457-W462
Authors: Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec, Tomáš Raček, Gabriela Bučeková, Dominik Tichý, Karel Berka, Radka Svobodová
Affiliations
- CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.
- Institute of Computer Science, Masaryk University, 602 00 Brno, Czech Republic.
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 779 00 Olomouc, Czech Republic.
Abstract
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 quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has no login requirement.
MeSH
Nucleic Acids