αCharges: partial atomic charges for AlphaFold structures in
high quality

J 2023

αCharges: partial atomic charges for AlphaFold structures in high quality

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ et. al.

Základní údaje

Originální název

αCharges: partial atomic charges for AlphaFold structures in high quality

Autoři

SCHINDLER, Ondřej (203 Česká republika, domácí), Karel BERKA (203 Česká republika), Alessio CANTARA (380 Itálie, domácí), Aleš KŘENEK (203 Česká republika, domácí), Dominik TICHÝ (203 Česká republika, domácí), Tomáš RAČEK (203 Česká republika, domácí) a Radka SVOBODOVÁ (203 Česká republika, garant, domácí)

Vydání

Nucleic Acids Research, Oxford, Oxford University Press, 2023, 0305-1048

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 14.900 v roce 2022

Kód RIV

RIV/00216224:14310/23:00130737

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1093/nar/gkad349

UT WoS

000984668800001

Klíčová slova anglicky

molecular structures; AlphaFoldDB; partial atomic charges; electrostatics; chemoinformatics

Štítky

CF BioData, J-D1, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 31. 10. 2024 10:48, Ing. Monika Szurmanová, Ph.D.

Anotace

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.

Návaznosti

LM2023054, projekt VaV

Název: e-Infrastruktura CZ

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, e-Infrastruktura CZ

MUNI/A/1413/2022, interní kód MU

Název: Struktura a dynamika biopolymerů

Investor: Masarykova univerzita, Struktura a dynamika biopolymerů

90255, velká výzkumná infrastruktura

Název: ELIXIR CZ III

Citovat

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ, Tomáš RAČEK a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Research. Oxford: Oxford University Press, 2023, roč. 51, W1, s. "W11"-"W16", 6 s. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad349.

@article{2281277,
   author = {Schindler, Ondřej and Berka, Karel and Cantara, Alessio and Křenek, Aleš and Tichý, Dominik and Raček, Tomáš and Svobodová, Radka},
   article_location = {Oxford},
   article_number = {W1},
   doi = {http://dx.doi.org/10.1093/nar/gkad349},
   keywords = {molecular structures; AlphaFoldDB; partial atomic charges; electrostatics; chemoinformatics},
   language = {eng},
   issn = {0305-1048},
   journal = {Nucleic Acids Research},
   title = {αCharges: partial atomic charges for AlphaFold structures in high quality},
   url = {https://doi.org/10.1093/nar/gkad349},
   volume = {51},
   year = {2023}
}

TY  - JOUR
ID  - 2281277
AU  - Schindler, Ondřej - Berka, Karel - Cantara, Alessio - Křenek, Aleš - Tichý, Dominik - Raček, Tomáš - Svobodová, Radka
PY  - 2023
TI  - αCharges: partial atomic charges for AlphaFold structures in high quality
JF  - Nucleic Acids Research
VL  - 51
IS  - W1
SP  - "W11"-"W16"
EP  - "W11"-"W16"
PB  - Oxford University Press
SN  - 03051048
KW  - molecular structures
KW  - AlphaFoldDB
KW  - partial atomic charges
KW  - electrostatics
KW  - chemoinformatics
UR  - https://doi.org/10.1093/nar/gkad349
N2  - 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.
ER  -

SCHINDLER, Ondřej, Karel BERKA, Alessio CANTARA, Aleš KŘENEK, Dominik TICHÝ, Tomáš RAČEK a Radka SVOBODOVÁ. αCharges: partial atomic charges for AlphaFold structures in high quality. \textit{Nucleic Acids Research}. Oxford: Oxford University Press, 2023, roč.~51, W1, s.~''W11''-''W16'', 6 s. ISSN~0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad349.

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