English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Plus monthly

Global: Zendy Tools annual

Global: Zendy Tools monthly

Global: Zendy Free Plan

COVID-19 has shown the importance of having a fast response againstpandemics. Finding a novel drug is a very long and complex procedure, and it ispossible to accelerate the preliminary phases by using computer simulations. Inparticular, virtual screening is an in-silico phase that is needed to filter alarge set of possible drug candidates to a manageable number. This paperpresents the implementations and a comparative analysis of two GPU-optimizedimplementations of a virtual screening algorithm targeting novel GPUarchitectures. The first adopts a traditional approach that spreads thecomputation required to evaluate a single molecule across the entire GPU. Thesecond uses a batched approach that exploits the parallel architecture of theGPU to evaluate more molecules in parallel, without considering the latency toprocess a single molecule. The paper describes the advantages and disadvantagesof the proposed solutions, highlighting implementation details that impact theperformance. Experimental results highlight the different performance of thetwo methods on several target molecule databases while running on NVIDIA A100GPUs. The two implementations have a strong dependency with respect to the datato be processed. For both cases, the performance is improving while reducingthe dimension of the target molecules (number of atoms and rotatable bonds).The two methods demonstrated a different behavior with respect to the size ofthe molecule database to be screened. While the latency one reaches sooner(with fewer molecules) the performance plateau in terms of throughput, thebatched one requires a larger set of molecules. However, the performances afterthe initial transient period are much higher (up to 5x speed-up). Finally, tocheck the efficiency of both implementations we deeply analyzed their workloadcharacteristics using the instruction roof-line methodology.

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