Publication details

Optimized SQE atomic charges for peptides accessible via a web application

Authors

SCHINDLER Ondřej RAČEK Tomáš MARŠAVELSKI Aleksandra KOČA Jaroslav BERKA Karel SVOBODOVÁ Radka

Year of publication 2021
Type Article in Periodical
Magazine / Source Journal of Cheminformatics
MU Faculty or unit

Central European Institute of Technology

Citation
Doi http://dx.doi.org/10.1186/s13321-021-00528-w
Keywords Partial atomic charges; Parameterization; Empirical methods; Web service
Description 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.
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