PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB
Structures

J 2025

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

SCHINDLER, Ondřej; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Gabriela BUČEKOVÁ et al.

Základní údaje

Originální název

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Autoři

SCHINDLER, Ondřej; Tomáš SVOBODA ; Adrián ROŠINEC ; Tomáš RAČEK; Gabriela BUČEKOVÁ ; Dominik TICHÝ; Karel BERKA a Radka SVOBODOVÁ

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2025, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 13.100 v roce 2024

Označené pro přenos do RIV

Ano

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

protein structure; partial atomic charges; quantum mechanical method GFN1-xTB

Štítky

143160, CF BioData, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 5. 2. 2026 10:40, Mgr. Eva Dubská

Anotace

V originále

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.

Návaznosti

EH23_015/0008210, projekt VaV

Název: ELIXIR CZ: Capacity extension

LM2023055, projekt VaV

Název: Česká národní infrastruktura pro biologická data

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, ELIXIR-CZ: Česká národní infrastruktura pro biologická data

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Citovat

SCHINDLER, Ondřej; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Gabriela BUČEKOVÁ; Dominik TICHÝ; Karel BERKA a Radka SVOBODOVÁ. PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. Nucleic Acids Research. Oxford: Oxford University Press, 2025, roč. 53, W1, s. "W457"-"W462", 6 s. ISSN 0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaf401.

@article{2500780,
   author = {Schindler, Ondřej and Svoboda, Tomáš and Rošinec, Adrián and Raček, Tomáš and Bučeková, Gabriela and Tichý, Dominik and Berka, Karel and Svobodová, Radka},
   article_location = {Oxford},
   article_number = {W1},
   doi = {https://doi.org/10.1093/nar/gkaf401},
   keywords = {protein structure; partial atomic charges; quantum mechanical method GFN1-xTB},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures},
   url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf401/8128216},
   volume = {53},
   year = {2025}
}

TY  - JOUR
ID  - 2500780
AU  - Schindler, Ondřej - Svoboda, Tomáš - Rošinec, Adrián - Raček, Tomáš - Bučeková, Gabriela - Tichý, Dominik - Berka, Karel - Svobodová, Radka
PY  - 2025
TI  - PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures
JF  - Nucleic Acids Research
VL  - 53
IS  - W1
SP  - "W457"-"W462"
EP  - "W457"-"W462"
PB  - Oxford University Press
SN  - 03051048
KW  - protein structure
KW  - partial atomic charges
KW  - quantum mechanical method GFN1-xTB
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf401/8128216
N2  - 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.
ER  -

SCHINDLER, Ondřej; Tomáš SVOBODA; Adrián ROŠINEC; Tomáš RAČEK; Gabriela BUČEKOVÁ; Dominik TICHÝ; Karel BERKA a Radka SVOBODOVÁ. PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2025, roč.~53, W1, s.~''W457''-''W462'', 6 s. ISSN~0305-1048. Dostupné z: https://doi.org/10.1093/nar/gkaf401.

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