PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F25%3A73633278" target="_blank" >RIV/61989592:15310/25:73633278 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216224:14740/25:00141272

Výsledek na webu

<a href="https://academic.oup.com/nar/article/53/W1/W457/8128216" target="_blank" >https://academic.oup.com/nar/article/53/W1/W457/8128216</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1093/nar/gkaf401" target="_blank" >10.1093/nar/gkaf401</a>

Jazyk výsledku

angličtina

Název v původním jazyce

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Popis výsledku v původním jazyce

The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has no login requirement.

Název v anglickém jazyce

PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures

Popis výsledku anglicky

The Protein Data Bank (PDB) is the largest database of experimentally determined protein structures, containing more than 230 000 experimentally determined structures. The chemical reactivity of proteins is based on the electron density distribution, which is usually approximated by partial atomic charges. However, because of the size and high variability, there is not yet a universal and accurate tool for calculating the partial atomic charges of these structures. For this reason, we introduce the web application PDBCharges: a tool for quick calculation of partial atomic charges for protein structures from PDB. The charges are calculated using the recent semi-empirical quantum-mechanical method GFN1-xTB, which reproduces PBE0/TZVP/CM5 charges. The computed partial atomic charges can be downloaded in common data formats or visualized online via the powerful Mol* Viewer. The PDBCharges application is freely available at https://pdbcharges.biodata.ceitec.cz and has 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

2025

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

53

Číslo periodika v rámci svazku

W1

Stát vydavatele periodika

GB - Spojené království Velké Británie a Severního Irska

Počet stran výsledku

6

Strana od-do

"W457"-"W462"

Kód UT WoS článku

001484543000001

EID výsledku v databázi Scopus

2-s2.0-105010285750