AlteQ: a new complementarity principle-centered method for the evaluation of docking poses

Abstract

Molecular docking is the most popular and widely used method for identifying novel molecules against a target of interest. However, docking procedures and their validation are still under intense development. In the present investigation, we evaluate a quantum free-orbital AlteQ method for evaluating docking complexes generated by taking EGFR complexes as an example. The AlteQ method calculates the electron density using Slater’s type atomic contributions in the interspace between the receptor and the ligand. Since the interactions are determined by the overlap of electron clouds, they follow the complementarity principle, and an equation can be obtained that describes these interactions. The AlteQ method evaluates the quality of the interaction between the receptor and the ligand, how complementary the interactions are, and due to this, it is used to reject less realistic structures obtained by docking methods. Here, three different equations were used to determine the quality of the interactions in experimental complexes and docked complexes obtained using AutoDock Vina and AutoDock 4.2.6.

Communicated by Ramaswamy H. Sarma

Keywords:

• Molecular docking
• AlteQ
• AutoDock Vina
• AutoDock 4.2.6
• complementarity principle

Authors’ contributions

M.A.G. and V.A.P. designed the study. S.K. and M.A.G. performed the analysis. J.N. designed and performed overlap analysis. H.R. and B.S.S performed data curation. S.K. and M.A.G. wrote the manuscript. All authors have given approval to the final version of the manuscript.

Data availability statement

The raw data are provided in Supplementary File 1. The AlteQ program is available free for download at www.chemosophia.com.

Disclosure statement

No conflict of interest has been reported by the authors.

Correction Statement

This article has been corrected with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This work was supported by the Ministry of Science and Higher Education of Russia (Grant FENU-2020-0019).