Analysis of docking algorithms by HPC methods generated in bioinformatics studies

¹ South-West University, Faculty of Engineering, Department of Electrotechnics, Electronics and Automation, Bulgaria
² American University in Bulgaria, Department of Computer Science, Bulgaria
³ South-West University, Faculty of Mathematics and Natural Science, Department of Informatics, Bulgaria
⁴ Bulgarian Academy of Sciences, Institute of Mathematics and Informatics, Bulgaria

^* Corresponding author: antonstoilov@swu.bg

Abstract

High-performance computing (HPC) is an important domain of the computer science field. For more than 30 years, it has allowed finding solutions to problems and enhanced progress in many scientific areas such as bioinformatics and drug design. The binding of small molecule ligands to large protein targets is central to numerous biological processes. The accurate prediction of the binding modes between the ligand and protein (the docking problem) is of fundamental importance in modern structure-based drug design. The interactions between the receptor and ligand are quantum mechanical in nature, but due to the complexity of biological systems, quantum theory cannot be applied directly. Consequently, most methods used in docking and computational drug discovery are more empirical in nature and usually lack generality.