Detailed Information on Publication Record
2023
αCharges: partial atomic charges for AlphaFold structures in high quality
SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ et. al.Basic information
Original name
αCharges: partial atomic charges for AlphaFold structures in high quality
Authors
SCHINDLER, Ondřej (203 Czech Republic, belonging to the institution), Karel BERKA (203 Czech Republic), Alessio CANTARA (380 Italy, belonging to the institution), Aleš KŘENEK (203 Czech Republic, belonging to the institution), Dominik TICHÝ (203 Czech Republic, belonging to the institution), Tomáš RAČEK (203 Czech Republic, belonging to the institution) and Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution)
Edition
Nucleic Acids Research, Oxford, Oxford University Press, 2023, 0305-1048
Other information
Language
English
Type of outcome
Článek v odborném periodiku
Field of Study
10201 Computer sciences, information science, bioinformatics
Country of publisher
United Kingdom of Great Britain and Northern Ireland
Confidentiality degree
není předmětem státního či obchodního tajemství
References:
Impact factor
Impact factor: 14.900 in 2022
RIV identification code
RIV/00216224:14310/23:00130737
Organization unit
Faculty of Science
UT WoS
000984668800001
Keywords in English
molecular structures; AlphaFoldDB; partial atomic charges; electrostatics; chemoinformatics
Tags
Tags
International impact, Reviewed
Změněno: 31/10/2024 10:48, Ing. Monika Szurmanová, Ph.D.
Abstract
V originále
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 αCharges: 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 αCharges application is freely available at https://alphacharges.ncbr.muni.cz with no login requirement.
Links
LM2023054, research and development project |
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MUNI/A/1413/2022, interní kód MU |
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90255, large research infrastructures |
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