AlphaFold at Scale: How PTP and AWS HealthOmics Transformed Protein Prediction

AWS Life Sciences, Blog

Overview

A vaccine company partnered with PTP to overcome the limitations of their on-premises AlphaFold deployment. By leveraging AWS HealthOmics, Amazon S3, and EC2, PTP delivered a scalable, high-performance solution that drastically accelerated protein structure prediction. The result: 12x faster workflows, 86% cost savings, and the ability to analyze 10x more complex proteins—transforming how this life sciences organization approaches discovery.

The Challenge: Resource Constraints Blocking Scientific Progress

Hardware Limitations

The company’s research teams struggled with limited access to GPUs, relying on laptops and legacy servers that couldn’t handle AlphaFold’s compute demands.

Storage Constraints

Inadequate on-premises storage prevented simultaneous access to lab datasets, slowing analysis and reducing research throughput.

Scaling Difficulties

As AlphaFold usage grew, their infrastructure couldn’t scale to meet demand, limiting the organization’s ability to support complex protein workflows.

Cloud Migration: Enabling Scalability and Flexibility

Data Migration to Amazon S3

PTP’s CloudOps team started by migrating all research data to Amazon S3, providing secure, scalable, and durable object storage.

EC2-Based AlphaFold Deployment

AlphaFold was deployed on Amazon EC2 instances to validate the viability of cloud-based compute infrastructure. Results showed parity with on-prem performance—opening the door to further optimization.

Performance Validation

Initial tests confirmed that the cloud-based system met or exceeded previous benchmarks. This milestone marked a turning point in adopting a fully cloud-native research stack.

Evaluating Cloud Tools: AWS Batch vs. AWS HealthOmics

AWS Batch

  • Offered flexible, custom workflows

  • Supported bespoke AlphaFold deployments

  • Required heavy manual configuration and management

AWS HealthOmics

  • Delivered native Nextflow integration

  • Included built-in bioinformatics tooling

  • Featured automated security and compliance

  • Reduced operational overhead through managed orchestration

PTP’s AWS consulting services guided the organization through this decision, ultimately selecting HealthOmics for its turnkey scalability and bioinformatics features.

Implementation: Supercharging AlphaFold with HealthOmics

Multiple High-Performance Servers

HealthOmics enabled distributed processing across multiple high-performance nodes, scaling beyond what on-premises systems could achieve.

GPU Acceleration

Multiple GPUs were used simultaneously—reducing model computation from days to hours.

Rapid Iteration

Improved infrastructure allowed for faster cycles of research and experimentation, accelerating results without compromising accuracy.

Customizing AlphaFold: Breaking Past Biological Barriers

Addressing Residue Limits

The standard AlphaFold model supports proteins up to 1,200 residues. This vaccine company needed to analyze proteins with over 12,000 residues.

Modifying AlphaFold

PTP’s cloud engineering team customized the AlphaFold source code to support extended residue lengths.

Adapting HealthOmics

Custom scripts were integrated into HealthOmics to run the enhanced AlphaFold pipeline—seamlessly maintaining workflow efficiency at scale.

 

Infrastructure Overview: Scalable, Secure, and Compliant

AWS HealthOmics Core

  • Centralized orchestration of bioinformatics pipelines

  • Seamless integration with AWS services

  • Enhanced security and life sciences compliance (HIPAA, GxP)

S3 Data Lake

  • Unified storage for raw datasets and results

  • Lifecycle management, versioning, and access control

  • Supports collaboration across teams and researchers

EC2 Compute Resources

 

  • GPU-powered on-demand computing

  • Flexible configurations tailored to workload needs

  • Rapid provisioning for experimental scaling

Transformative Results

Metric Improvement
Workflow Speed 12x Faster
Cost Savings 86% Reduction
Protein Complexity 10x More Residues

By scaling AlphaFold in the cloud and tailoring it to scientific needs, PTP helped this life sciences company remove computational barriers, reduce costs, and accelerate discovery.

Accelerate your scientific research with cloud infrastructure built for life sciences.

PTP combines AWS HealthOmics, secure architecture, and managed cloud services for life sciences to reduce cost and speed discovery.

👉 Request your Free Cloud Assessmentor explore👉 PTP's AWS Marketplace Offers