PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures DOI Creative Commons
Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: unknown

Published: May 10, 2025

Abstract The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 structures. chemical reactivity proteins based on electron density distribution, which usually approximated by partial atomic charges. However, because size and high variability, there not yet a universal accurate tool for calculating charges these For this reason, we introduce web application PDBCharges: quick calculation structures from PDB. are calculated using recent semi-empirical quantum-mechanical method GFN1-xTB, reproduces PBE0/TZVP/CM5 computed can be downloaded in common data formats or visualized online via powerful Mol* Viewer. PDBCharges freely available at https://pdbcharges.biodata.ceitec.cz has no login requirement.

Language: Английский

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures DOI Creative Commons
Ondřej Schindler, Tomáš Svoboda, Adrián Rošinec

et al.

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: unknown

Published: May 10, 2025

Abstract The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 structures. chemical reactivity proteins based on electron density distribution, which usually approximated by partial atomic charges. However, because size and high variability, there not yet a universal accurate tool for calculating charges these For this reason, we introduce web application PDBCharges: quick calculation structures from PDB. are calculated using recent semi-empirical quantum-mechanical method GFN1-xTB, reproduces PBE0/TZVP/CM5 computed can be downloaded in common data formats or visualized online via powerful Mol* Viewer. PDBCharges freely available at https://pdbcharges.biodata.ceitec.cz has no login requirement.

Language: Английский

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