Created by: MinGyu Choi Last modified: Jan14 2022 Contact: [email protected] | [email protected]

This Notion page deals with three methods for using AlphaFold2 in both local environment and cloud-computing environment (Amazon cloud and Google colab).

You can easily build your protein structure prediction environment by reproducing following instructions in this page.

(For BHI-members) I already constructed AlphaFold2 environment in both bhi3 and bhi4 server: you can easily use AlphaFold2 without setting a new environment. Indeed, AlphaFold2 requires > 3 TB storage → if you want to use AlphaFold2, please contact me and use the environment I am using now. If nobody wants to use AlphaFold2 at the time I leave the lab, I will remove all data I constructed.

Please feel free to contact me if you faced an error or if you have any suggestions.

0. Overview / References

1. Colab AlphaFold2

2. AWS Server Setup

3. Package Setup

4. Download af_download_data

5. Run CPU part (MSA)

6. Run GPU part (evoformer + structure module)