Recent Advances in Computer-aided Virtual Screening and Docking Optimization for Aptamer

Abstract

Aptamers, as artificially synthesized short nucleotide sequences, have been widely used in protein analysis, gene engineering, and molecular diagnostics. Currently, the screening process of aptamers still relies on the traditional SELEX process, which is cumbersome and complex. Moreover, the success rate of aptamer screening through the SELEX process is not high, which has become a major challenge. In recent years, the development of computers has facilitated virtual screening, which can greatly accelerate the screening process of aptamers through computer-assisted screening. However, the accuracy and precision of current virtual screening software on the market vary. Therefore, this work summarizes the docking characteristics of four mainstream molecular docking software programs, including Auto dock, Auto dock Vina, MOE, and hex Dock, in recent years. Moreover, the accuracy and prediction performance of these four molecular docking software programs for aptamer docking based on experimental data is also evaluated. This will guide researchers in the selection of molecular docking software. Additionally, this review provides a detailed overview of the application of computer-aided virtual screening in aptamer screening, thus providing a direction for future development in this field.

Keywords: Aptamers; Computer-aided drug design; Molecular docking; Optimization; SELEX; Virtual screening.