Boost Protein Structure Prediction in AlphaFold2 with Cloud HPC

AlphaFold2 is a groundbreaking AI software developed by DeepMind, Inc. On November 30, 2020, the software predicted most protein structures in the protein structure prediction competition CASP 14 that were only one atom's width away from the real structure, reaching the level of predictions observed by humans using sophisticated instruments such as cryo-electron microscopy, which is an unprecedented and tremendous progress in protein structure prediction.

boost protein structure prediction in AlphaFold2 with AWS, Google Cloud, Azure high performance computing

The source code of AlphaFold2 is now publicly available on GitHub. Many scientists are now using AlphaFold2 to make high-throughput predictions on existing protein databases, building a database of AlphaFold2 predicted structures for all proteins of some model organism species. (

We can see that although all protein databases are not covered although multiple databases of different species are predicted with AlphaFold2. Only by building AlphaFold locally, can we predict the protein structures that we are interested in anytime.

This article elaborates on 2 approaches to using AlphaFold2. On the one hand, you can log in to Cloudam where AlphaFold2 is pre-installed, and submit protein structure jobs in just a minute. Moreover, the template submission is very user-friendly to beginners who are not that familiar with command lines. On the other hand, AlphaFold2 can also be installed locally. However, this requires a more comprehensive skillset in Linux, and errors may occur from time to time.

Predict Protein Structure in AlphaFold2 with Cloudam

Video tutorial of how to run AlphaFold2 on cloud-HPC platform

1. Find AlphaFold2 on Cloudam

After logging in, it is pretty easy to find Alphafold2 in the 'Applications' center. Click on it and then choose 'Submit'.

2. Select Visualization Template

It is highly recommended to use the Visualization Template since jobs can be efficiently submitted with just a few clicks setting a few parameters.

3. Submit a job with a few clicks

Upload a .fasta file. Select 'monomer' if the input file is monolithic, and "multimer" if it is polymorphic.

After setting up, you can choose the GPUs according to your needs.

You can submit the job after checking the summary of the job.

4. Check the job and its result

The job can be checked and monitored on 'My jobs'.