PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F25%3A73633278" target="_blank" >RIV/61989592:15310/25:73633278 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/25:00141272
Result on the web
<a href="https://academic.oup.com/nar/article/53/W1/W457/8128216" target="_blank" >https://academic.oup.com/nar/article/53/W1/W457/8128216</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkaf401" target="_blank" >10.1093/nar/gkaf401</a>
Alternative languages
Result language
angličtina
Original language name
PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures
Original language description
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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2025
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
NUCLEIC ACIDS RESEARCH
ISSN
0305-1048
e-ISSN
1362-4962
Volume of the periodical
53
Issue of the periodical within the volume
W1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
6
Pages from-to
"W457"-"W462"
UT code for WoS article
001484543000001
EID of the result in the Scopus database
2-s2.0-105010285750