APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

TL;DR

APACE leverages AlphaFold2 and supercomputing to drastically accelerate protein structure prediction, reducing analysis time from weeks to minutes and enabling faster scientific discoveries in biophysics.

Contribution

This paper introduces APACE, a novel framework that integrates AlphaFold2 with advanced supercomputing resources to significantly speed up protein structure prediction processes.

Findings

APACE is up to 100 times faster than standard AlphaFold2 implementations.

It successfully predicts structures for multiple proteins using thousands of GPU cores.

The framework is deployable on modern supercomputers like Delta and Polaris.

Abstract

The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics, and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these novel AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a novel computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers, and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.