Optimized SQE atomic charges for peptides accessible via a web application

Varování

Publikace nespadá pod Ústav výpočetní techniky, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.

Autoři	SCHINDLER Ondřej RAČEK Tomáš MARŠAVELSKI Aleksandra KOČA Jaroslav BERKA Karel SVOBODOVÁ Radka
Rok publikování	2021
Druh	Článek v odborném periodiku
Časopis / Zdroj	Journal of Cheminformatics
Fakulta / Pracoviště MU	Středoevropský technologický institut
Citace
www	https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00528-w
Doi	http://dx.doi.org/10.1186/s13321-021-00528-w
Klíčová slova	Partial atomic charges; Parameterization; Empirical methods; Web service
Popis	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.