αCharges: partial atomic charges for AlphaFold structures in high quality

Kód výsledku v 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>

Nalezeny alternativní kódy

RIV/00216224:14310/23:00130737

Výsledek na webu

<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>

Jazyk výsledku

angličtina

Název v původním jazyce

αCharges: partial atomic charges for AlphaFold structures in high quality

Popis výsledku v původním jazyce

The AlphaFold2 prediction algorithm opened up the possibility of exploring proteins&apos; structural space at an unprecedented scale. Currently, &gt;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.

Název v anglickém jazyce

αCharges: partial atomic charges for AlphaFold structures in high quality

Popis výsledku anglicky

The AlphaFold2 prediction algorithm opened up the possibility of exploring proteins&apos; structural space at an unprecedented scale. Currently, &gt;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.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10403 - Physical chemistry

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2023

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

NUCLEIC ACIDS RESEARCH

ISSN

0305-1048

e-ISSN

1362-4962

Svazek periodika

51

Číslo periodika v rámci svazku

W1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

6

Strana od-do

"W11–W16"

Kód UT WoS článku

000984668800001

EID výsledku v databázi Scopus

2-s2.0-85164242994