αCharges: partial atomic charges for AlphaFold structures in high quality

Varování

Publikace nespadá pod Pedagogickou fakultu, ale pod Přírodovědeckou fakultu. Oficiální stránka publikace je na webu muni.cz.
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SCHINDLER Ondřej BERKA Karel CANTARA Alessio KŘENEK Aleš TICHÝ Dominik RAČEK Tomáš SVOBODOVÁ Radka

Rok publikování 2023
Druh Článek v odborném periodiku
Časopis / Zdroj Nucleic Acids Research
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
www https://doi.org/10.1093/nar/gkad349
Doi http://dx.doi.org/10.1093/nar/gkad349
Klíčová slova molecular structures; AlphaFoldDB; partial atomic charges; electrostatics; chemoinformatics
Popis 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 ?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 ?Charges application is freely available at https://alphacharges.ncbr.muni.cz with no login requirement.
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