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.

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:

URL

Impact factor

Impact factor: 14.900 in 2022

RIV identification code

RIV/00216224:14310/23:00130737

Organization unit

Faculty of Science

DOI

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

UT WoS

000984668800001

Keywords in English

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

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

Name: e-Infrastruktura CZ

Investor: Ministry of Education, Youth and Sports of the CR

LM2023055, research and development project

Name: Česká národní infrastruktura pro biologická data

Investor: Ministry of Education, Youth and Sports of the CR, ELIXIR-CZ: Czech National Infrastructure for Biological Data

MUNI/A/1413/2022, interní kód MU

Name: Struktura a dynamika biopolymerů

Investor: Masaryk University

Citovat

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

Detailed Information on Publication Record