Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App

Gadioli, Davide; Palermo, Gianluca; Cherubin, Stefano; Vitali, Emanuele; Agosta, Giovanni; Manelfi, Candida; Beccari, Andrea R.; Cavazzoni, Carlo; Sanna, Nico; Silvano, Cristina

Abstract

The drug discovery process involves several tasks to be performed in vivo, in vitro and in silico. Molecular docking is a task typically performed in silico. It aims at finding the three-dimensional pose of a given molecule when it interacts with the target protein binding site. This task is often done for virtual screening a huge set of molecules to find the most promising ones, which will be forwarded to the later stages of the drug discovery process. Given the huge complexity of the problem, molecular docking cannot be solved by exploring the entire space of the ligand poses. State-of-the-art approaches face the problem by sampling the space of the ligand poses to generate results in a reasonable time budget. In this work, we improve the geometric approach to molecular docking by introducing tunable approximations. In particular, we analysed and enriched the original implementation with tunable software knobs to explore and control the performance-accuracy trade-offs. We modelled time-to-solution of the virtual screening task as a function of software knobs, input data features, and available computational resources. Therefore, the application can autotune its configuration according to a user-defined time budget. We used a Mini-App derived by LiGenDock—a state-of-the-art molecular docking application—to validate the proposed approach. We run the enhanced Mini-App on a high-performance computing system by using a very large database of pockets and ligands. The proposed approach exposes a time-to-solution interval spanning more than one order of magnitude with accuracy degradation up to 30%, more in general providing different accuracy levels according to the needs of the virtual screening campaign.

Citation

Gadioli, D., Palermo, G., Cherubin, S., Vitali, E., Agosta, G., Manelfi, C., Beccari, A. R., Cavazzoni, C., Sanna, N., & Silvano, C. (2021). Tunable approximations to control time-to-solution in an HPC molecular docking Mini-App. Journal of Supercomputing, 77(1), 841-869. https://doi.org/10.1007/s11227-020-03295-x

• Journal Article Type: Article
• Online Publication Date: Apr 29, 2020
• Publication Date: 2021-01
• Deposit Date: Jun 19, 2021
• Journal: The Journal of Supercomputing
• Print ISSN: 0920-8542
• Electronic ISSN: 1573-0484
• Publisher: Springer
• Peer Reviewed: Peer Reviewed
• Volume: 77
• Issue: 1
• Pages: 841-869
• DOI: https://doi.org/10.1007/s11227-020-03295-x
• Keywords: Autotuning, Molecular docking, Performance model, Approximate computing
• Public URL: http://researchrepository.napier.ac.uk/Output/2781711