αCharges: partial atomic charges for AlphaFold structures in high quality
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F23%3A73621476" target="_blank" >RIV/61989592:15310/23:73621476 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14310/23:00130737
Result on the web
<a href="https://academic.oup.com/nar/article/51/W1/W11/7157525" target="_blank" >https://academic.oup.com/nar/article/51/W1/W11/7157525</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1093/nar/gkad349" target="_blank" >10.1093/nar/gkad349</a>
Alternative languages
Result language
angličtina
Original language name
αCharges: partial atomic charges for AlphaFold structures in high quality
Original language description
The AlphaFold2 prediction algorithm opened up the possibility of exploring proteins' structural space at an unprecedented scale. Currently, >200 million protein structures predicted by this approach are deposited in AlphaFoldDB, covering entire proteomes of multiple organisms, including humans. Predicted structures are, however, stored without detailed functional annotations describing their chemical behaviour. Partial atomic charges, which map electron distribution over a molecule and provide a clue to its chemical reactivity, are an important example of such data. We introduce the web application alpha Charges: a tool for the quick calculation of partial atomic charges for protein structures from AlphaFoldDB. The charges are calculated by the recent empirical method SQE+qp, parameterised for this class of molecules using robust quantum mechanics charges (B3LYP/6-31G*/NPA) on PROPKA3 protonated structures. The computed partial atomic charges can be downloaded in common data formats or visualised via the powerful Mol* viewer. The alpha Charges application is freely available at https://alphacharges.ncbr.muni.cz with 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
2023
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
51
Issue of the periodical within the volume
W1
Country of publishing house
GB - UNITED KINGDOM
Number of pages
6
Pages from-to
"W11–W16"
UT code for WoS article
000984668800001
EID of the result in the Scopus database
2-s2.0-85164242994