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v1.13.4 #49

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Update README
brianloyal Dec 29, 2025
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v1.13.4
brianloyal Dec 29, 2025
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brianloyal Dec 29, 2025
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

---

## [1.13.4] - 2025-12-29

### 1.13.4 Fixed

- Fixed broken links and added region information to README

---

## [1.13.3] - 2025-10-14

### 1.13.3 Updates
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30 changes: 13 additions & 17 deletions README.md
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Expand Up @@ -3,6 +3,9 @@
> [!IMPORTANT]
> The examples provided in this repository are for experimental and educational purposes only. They demonstrate concepts and techniques but are not intended for direct use in production environments.

> [!IMPORTANT]
> The CloudFormation templates included in this repository only support deployment to the us-east-1, and us-east-2, eu-west-1, eu-west-2, eu-central-1, and ap-southwest-1 regions. For additional options, please refer to the [Drug Discovery Workflows for AWS HealthOmics](https://github.com/aws-samples/drug-discovery-workflows) project.

## Contents

1. [Overview](#1-overview)
Expand All @@ -16,10 +19,10 @@
4.2. [AlphaFold](#42-alphafold)
4.3. [OpenFold](#43-openfold)
4.4. [OmegaFold](#44-omegafold)
4.5. [ESMFold](#46-esmfold)
4.6. [ProteinMPNN](#47-proteinmpnn)
4.7. [DiffDock](#48-diffdock)
4.8. [RFDiffusion](#49-rfdiffusion)
4.5. [ESMFold](#45-esmfold)
4.6. [ProteinMPNN](#46-proteinmpnn)
4.7. [DiffDock](#47-diffdock)
4.8. [RFDiffusion](#48-rfdiffusion)
5. [Architecture Details](#5-architecture-details)
5.1. [Stack Creation Details](#51-stack-creation-details)
5.2. [Cost](#52-cost)
Expand All @@ -43,18 +46,11 @@ This repository includes the CloudFormation template, Jupyter Notebook, and supp

## 2. Quick Start

1. Choose **Launch Stack** and (if prompted) log into your AWS account:

| Region | Launch URL |
| ------ | ---------- |
| eu-west-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
| eu-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
| eu-central-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://eu-central-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-eu-central-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
| ap-southeast-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://ap-southeast-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-ap-southeast-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
| us-east-1 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-east-1.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-east-1.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
| us-west-2 | [![Launch Stack](imgs/LaunchStack.jpg)](https://us-west-2.console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://5d1a4b76751b4c8a994ce96bafd91ec9-us-west-2.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml) |
NOTE: This procedure only supports the following AWS regions: eu-west-1, eu-west-2, eu-central-1, ap-southwest-1, us-east-1, and us-east-2

2. For **Stack Name**, enter a value unique to your account and region. Also update the *DeploymentRegion** parameter with the name of your current AWS region. Leave the other parameters as their default values and select **Next**.
1. Choose **Launch Stack** and (if prompted) log into your AWS account:
[![Launch Stack](imgs/LaunchStack.jpg)](https://console.aws.amazon.com/cloudformation/home#/stacks/create/review?templateURL=https://aws-hcls-ml.s3.amazonaws.com/main/batch-protein-folding-cfn-packaged.yaml)
2. For **Stack Name**, enter a value unique to your account and region. Leave the other parameters as their default values and select **Next**.
![Provide a stack name](imgs/name.png)
3. Select **I acknowledge that AWS CloudFormation might create IAM resources with custom names**.
4. Choose **Create stack**.
Expand Down Expand Up @@ -113,9 +109,9 @@ Please visit [https://github.com/EddyRivasLab/hmmer](https://github.com/EddyRiva

### 4.2. AlphaFold

Please visit [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold) for more information about the AlphaFold2 algorithm.
[Version 2.3.2](https://github.com/deepmind/alphafold/releases/tag/v2.3.2) from 4/5/2023.

Due to updates to the OpenMM module, GPU-accelerated relaxation is no longer available. All alphafold jobs now default to `use_gpu_relax=False`.
Please visit [https://github.com/deepmind/alphafold](https://github.com/deepmind/alphafold) for more information about the AlphaFold2 algorithm.

The original AlphaFold 2 citation is

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