CASE STUDY
Ampere®-powered ALAFIA Supercomputer Speeds Drug–Protein Binding Simulations at University of Miami
Ampere®-powered ALAFIA Supercomputer Speeds Drug–Protein Binding Simulations at University of Miami
21 May 2025
21 May 2025
INTRODUCTION
Imagine accelerating critical drug discovery simulations from over a day to mere hours. The University of Miami’s Systems Drug Discovery Lab achieved exactly this, transforming their research into protein–ligand binding and therapeutic modeling. By integrating ALAFIA’s AIVAS Supercomputer, powered by the AmpereOne® 192-core processor, they unlocked unprecedented efficiency, deeper molecular insights, and a faster path to breakthrough therapies. Discover how this powerful collaboration is revolutionizing early-stage drug development.
COMPANY DESCRIPTION
The University of Miami Frost Institute for Data Science and Computing’s Systems Drug Discovery Lab develops computational methods to support early-stage therapeutic research in cancer, infectious diseases, and other areas. The lab integrates physics-based modeling, AI-driven prediction, and large-scale data analysis to study protein–ligand binding, ternary complex formation, and other key drug-discovery processes. Its interdisciplinary approach—combining molecular simulation, cheminformatics, and machine learning—enables high-throughput, structure-informed strategies for identifying and refining novel therapeutic candidates.
Challenge
The University of Miami's Lab faced computationally intensive workloads, including long molecular dynamics simulations and PROTAC predictions. Shared university computing infrastructure hindered rapid iteration and streamlined exploratory modeling. This created bottlenecks, limiting timely analysis for targets across cancer and infectious diseases, impacting their high-throughput research pipeline.
Solution
The Lab incorporated ALAFIA’s AIVAS Supercomputer, powered by the AmpereOne 192-core processor,. This dedicated system enabled rapid, highly parallelized molecular dynamics simulations without reconfiguring workflows or relying on shared compute queues. Researchers now seamlessly prototype and perform iterative analysis across multiple targets.
Benefits
The Lab achieved up to a 10x1 reduction in simulation runtime, enabling broader, deeper analysis of protein–ligand interactions. Dedicated high-performance access simplified modeling, extended simulation windows, and accelerated Python analytics. This delivered richer structural insights while maintaining energy efficiency, supporting faster therapeutic research.
“ALAFIA’s AIVAS Supercomputer, powered by Ampere’s processor, made it significantly easier for us to run our routine molecular simulations more efficiently and with fewer barriers. This system gave us additional flexibility to explore protein–ligand binding and complex formation, particularly in our studies of targeted protein degraders.”
— Dr. Stephan Schürer
Professor, Department of Pharmacology, Miller School of Medicine, University of Miami
“Our AIVAS Supercomputer was purpose-built to harness Ampere’s compute-dense, power-efficient architecture. Ampere-powered systems like ALAFIA represent an important step toward democratizing access to high-performance computing—removing the need for complex clusters or costly cloud setups. That kind of accessibility doesn’t just simplify workflows—it accelerates innovation. In our case, it enables advanced simulations that drive early-stage drug development forward.”
— Camilo Buscaron
CEO, ALAFIA
References
1. Performance comparison based on internal benchmarks conducted by the University of Miami’s Frost Institute for Data Science and Computing, Systems Drug Discovery Lab (the customer), in February 2025. Results reflect measured reductions in runtime for key simulations comparing the Ampere/Alafia system to the lab’s existing HPC cluster-based solutions. All findings were generated and validated by the custom.
About Ampere
Ampere is a semiconductor design company for a new era, leading the future of computing with an innovative approach to CPU design focused on high-performance, energy efficient AI compute. As a pioneer in the new frontier of energy efficient high-performance computing, Ampere is part of the Softbank Group of companies driving sustainable computing for AI, Cloud, and edge applications.
See our solutions for a variety of demanding workloads: amperecomputing.com/solutions
Visit our Developer Center: amperecomputing.com/developers
Disclaimer
All data and information contained in Disclaimer: All data and information contained in or disclosed by this document are for informational purposes only and
are subject to change. This document may contain technical inaccuracies, omissions and typographical errors, and Ampere is under no obligation to update
or correct this information. Ampere makes no representations or warranties of any kind, including express or implied guarantees of noninfringement,
merchantability, or fitness for a particular purpose, and assumes no liability of any kind. All information is provided “AS IS.” This document is not an offer or a
binding commitment by Ampere.
This document is not to be used, copied, or reproduced in its entirety, or presented to others without the express written permission of Ampere®.
© 2026 Ampere® Computing LLC. All rights reserved. Ampere®, Ampere® Computing, Altra and the Ampere® logo are all trademarks of Ampere® Computing LLC or its affiliates. Other product names used in this publication are for identification purposes only and may be trademarks of their respective companies.
Ampere Computing LLC
4655 Great America Parkway Suite 601
Santa Clara, CA 95054
