xTrimoMultimer

Figure: Comparison of xTrimoMultimer's prediction to the predicted structure of AlphaFold2-Multimer on PDB 3G6D.

Optimizing Protein Structure Prediction Model for both monomer and multimer on GPU Clusters

xTrimoMultimer is a cooperation project by BioMap and HPC-AI TECH which provides a high-performance implementation of AlphaFold and AlphaFold Multimer with the following characteristics.

1. Fast kernel performance on GPU platform.
2. Supporting Various Parallelism including Dynamic Axial Parallelism(DAP) by FastFold in multi-GPU environment for both AlphaFold monomer and multimer.
3. Support long sequence training(To be supported in the future) and inference in both monomer and multimer.

Quick start

We strongly recommend users follow this installation manual step by step.

Choosing the way you feel comfortable between container environment and non-container environment. We have provide both way for users to make choice.

Installation

With existing conda

Create the virtual environment by the environment.yaml we provide:

conda create -n xtrimomultimer -f requirements/environment.yaml

Noticed that one of the dependencies colossalai may need CUDA Toolkit to be correctly installed. Installation under machine without NVIDIA GPU and CUDA thus may fail.

We will add a further switch to handle this problem.

Patch Openmm

(Please change the [PATH_TO_ENV] to the envs path)

pushd [PATH_TO_ENV]/lib/python3.7/site-packages/ && patch -p0 < ./lib/openmm.patch && popd

Activate the environment

conda activate xtrimomultimer

Compile the acceleration modules

Execute the following commands to compile the acceleration modules after first activation of your environment.

python setup.py install

With Docker

To use container for reducing the influence of difference system package/configuration, a Dockerfile is provided. Since this dockerfile is written in version 1.4 of Dockerfile syntax version, we need a extention provided by the Docker officially. If you cannot find the command docker buildx, a detailed manual installation guide on this extension can be found in this webpage.

The building command for the container is:

docker buildx build . --file Dockerfile --tag xtrimomultimer:latest

Usage

Development

In general, to avoid affect of different hardware/system package, we strongly recommended to develop in a virtual machine or container.

There are also some pakcage useful during development that can be installed through pip:

pip install -r requirements/dev.txt

Before PR

In order to make the codes in this repo be consistent and easy to read. We use pre-commit to manage the format issues all around the project codes. We strongly recommend to execute the following command under the root directory of project after installing packages in Development section:

pre-commit run --all-files

Inference

Please specify the cuda_device, fasta_paths and output_dir, then execute the following bash, all the results will be saved in output_dir.

Use the following script to see the usage of inference.py

python inference.py --help

A sample running script has been put into bin/inference.sh for reference.

Test

Prepare

To running all the test cases, you need to install extra packages to install test environ requirements.

Use the following command to install the test requirements:

pip install -r requirements/test.txt

Running Test Cases

To running all the test cases, execute the following command under the vritual environment:

# Add -v for verbose mode
pytest [the_path_to_special_test_file] [-v]

Or with extra coverage command to generate code coverage report:

coverage run -m pytest [the_path_to_special_test_file]
coverage report -m

Indicators in [] can be ignored or deleted to run all the test cases.

Copyright Notice

Caution: To deprecate our inner feature processing logics, OpenFold's data processing code has been greatly introduced before feature_processing parts. This may cause some problems, because the open source version of OpenFold's multimer has not yet published with comprehensive test. If there exists any problem on data processing parts, please feel free to leave a message on Issues page.

Code License

AlphaFold's, OpenFold's and, by extension, xTrimoMultimer source code is licensed under the permissive Apache Licence, Version 2.0.

Model Parameters License

The official AlphaFold parameters are made available under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) license.

Third-party Software License

Use of the third-party software, libraries or code referred to in the Acknowledgements section above may be governed by separate terms and conditions or license provisions.

Your use of the third-party software, libraries or code is subject to any such terms and you should check that you can comply with any applicable restrictions or terms and conditions before use.

Reference

• AlphaFold, Jumper, John and Evans, Richard, etc., 2021

• AlphaFold Multimer, Evans, Richard and ONeill, Michael, etc., 2022

• OpenFold, Ahdritz, Gustaf and Bouatta, etc., 2021

• FastFold, Shenggan Cheng, Ruidong Wu and Zhongming Yu, etc., 2022

Acknowledgements

xTrimoMultimer uses and/or references the following separate libraries and packages (ordered alphabetically):

• Biopython
• ColossalAI
• DeepSpeed
• Docker
• einops
• HH Suite
• HMMER Suite
• Kalign
• ML Collections
• NumPy
• OpenMM
• Pandas
• PDBFixer
• Pytorch
• PyTorch Lightning
• PyYAML
• Scipy
• Tqdm
• Tree

Thanks for all their contributors and maintainers!