Optimized SQE atomic charges for peptides accessible via a web application

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F21%3A73610418" target="_blank" >RIV/61989592:15310/21:73610418 - isvavai.cz</a>

Alternative codes found

RIV/00216224:14740/21:00121862

Result on the web

<a href="https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w.pdf" target="_blank" >https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-021-00528-w.pdf</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13321-021-00528-w" target="_blank" >10.1186/s13321-021-00528-w</a>

Result language

angličtina

Original language name

Optimized SQE atomic charges for peptides accessible via a web application

Original language description

Background: Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations-e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible. Results: In this article, we present for the first time an optimized guided minimization method (optGM) for the fast parameterization of empirical charge calculation methods and compare it with the currently available guided minimization (GDMIN) method. Then, we introduce a further extension to SQE, SQE+qp, adapted for peptide datasets, and compare it with the common approaches EEM, QEq EQeq, SQE, and SQE+q0. Finally, we integrate SQE and SQE+qp into the web application Atomic Charge Calculator II (ACC II), including several parameter sets. Conclusion: The main contribution of the article is that it makes SQE methods with their parameters accessible to the users via the ACC II web application (https://acc2.ncbr.muni.cz) and also via a command-line application. Furthermore, our improvement, SQE+qp, provides an excellent solution for peptide datasets. Additionally, optGM provides comparable parameters to GDMIN in a markedly shorter time. Therefore, optGM allows us to perform parameterizations for charge calculation methods with more parameters (e.g., SQE and its extensions) using large datasets.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

<a href="/en/project/LM2018131" target="_blank" >LM2018131: Czech National Infrastructure for Biological Data</a><br>

Continuities

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

Publication year

2021

Confidentiality

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

Name of the periodical

Journal of Cheminformatics

ISSN

1758-2946

e-ISSN

—

Volume of the periodical

13

Issue of the periodical within the volume

1

Country of publishing house

GB - UNITED KINGDOM

Number of pages

11

Pages from-to

"45-1"-"45-11"

UT code for WoS article

000668532100001

EID of the result in the Scopus database

2-s2.0-85108915985