GPU-optimized Approaches to Molecular Docking-based Virtual Screening in Drug Discovery: A Comparative Analysis

TL;DR

This paper compares two GPU-optimized virtual screening methods for drug discovery, analyzing their performance and efficiency on NVIDIA A100 GPUs, highlighting their advantages, limitations, and suitability based on molecule database size.

Contribution

It introduces and evaluates two novel GPU-based virtual screening implementations, providing insights into their performance trade-offs and optimization strategies for drug discovery.

Findings

Batched approach achieves up to 5x speed-up over latency approach.

Performance depends on molecule size and database scale.

Deep workload analysis using instruction roof-line methodology.

Abstract

COVID-19 has shown the importance of having a fast response against pandemics. Finding a novel drug is a very long and complex procedure, and it is possible to accelerate the preliminary phases by using computer simulations. In particular, virtual screening is an in-silico phase that is needed to filter a large set of possible drug candidates to a manageable number. This paper presents the implementations and a comparative analysis of two GPU-optimized implementations of a virtual screening algorithm targeting novel GPU architectures. The first adopts a traditional approach that spreads the computation required to evaluate a single molecule across the entire GPU. The second uses a batched approach that exploits the parallel architecture of the GPU to evaluate more molecules in parallel, without considering the latency to process a single molecule. The paper describes the advantages and disadvantages of the proposed solutions, highlighting implementation details that impact the performance. Experimental results highlight the different performance of the two methods on several target molecule databases while running on NVIDIA A100 GPUs. The two implementations have a strong dependency with respect to the data to be processed. For both cases, the performance is improving while reducing the dimension of the target molecules (number of atoms and rotatable bonds). The two methods demonstrated a different behavior with respect to the size of the molecule database to be screened. While the latency one reaches sooner (with fewer molecules) the performance plateau in terms of throughput, the batched one requires a larger set of molecules. However, the performances after the initial transient period are much higher (up to 5x speed-up). Finally, to check the efficiency of both implementations we deeply analyzed their workload characteristics using the instruction roof-line methodology.