File size: 2,966 Bytes
35cdf53 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 | # AlphaFold 3 Integration for OneScience
This is the AlphaFold 3 implementation integrated into the OneScience framework as a submodule.
## Overview
AlphaFold 3 is a state-of-the-art machine learning model for predicting protein structure, developed by DeepMind. This submodule integrates AlphaFold 3 into the OneScience framework, allowing it to be used as part of larger scientific computing workflows.
## Installation
### As Part of OneScience
The recommended way to install alphafold3 is as part of the complete OneScience package:
```bash
# Install OneScience with alphafold3 support
# install jackhmmer
# mkdir ~/hmmer_build ~/hmmer
# wget http://eddylab.org/software/hmmer/hmmer-3.4.tar.gz --directory-prefix ~/hmmer_build
# cd ~/hmmer_build && tar zxf hmmer-3.4.tar.gz && rm hmmer-3.4.tar.gz
# patch -p0 < jackhmmer_seq_limit.patch
# cd ~/hmmer-3.4
# ./configure --prefix ~/hmmer
# make -j && make install && cd ./easel && make install
# rm -R ~/hmmer_build
# # install extension
# pip install .[bio] -c constraints.txt
# cp -r /public/onestore/onedatasets/alphafold3/_dep xxx/
# export ALPHAFOLD3_DEP_DIR=/public/onestore/onedatasets/alphafold3/_dep
# cd src/onescience/flax_models/alphafold3/
# python build_extension.py
# optional create mmseqs2 database (please contact ai4s@sugon.com for mmseqs2 program)
export mmfasta=/root/public_databases
cd /root/public_databases && mkdir mmseqsDB
export mmdb=/root/public_databases/mmseqsDB
export CUDA_VISIBLE_DEVICES=0
mmseqs createdb $mmfasta/bfd-first_non_consensus_sequences.fasta $mmdb/small_bfd_db --gpu 1 --threads 32 --createdb-mode 2
mmseqs createdb $mmfasta/mgy_clusters_2022_05.fa $mmdb/mgnify_db --gpu 1 --threads 32 --createdb-mode 2
mmseqs createdb $mmfasta/uniprot_all_2021_04.fa $mmdb/uniprot_cluster_annot_db --gpu 1 --threads 32 --createdb-mode 2
mmseqs createdb $mmfasta/uniref90_2022_05.fa $mmdb/uniref90_db --gpu 1 --threads 32 --createdb-mode 2
```
## Usage
```python
# Import alphafold3 as part of onescience
import flax_model.alphafold3 as af3
# Access alphafold3 components
from flax_model.alphafold3 import structure, model, data
# Use alphafold3 functionality
print(f"AlphaFold3 version: {af3.__version__}")
```
## Requirements
- Python 3.11+
- JAX with CUDA support (optional, for GPU acceleration)
- CMake 3.28+ (for building C++ extensions)
- Additional dependencies listed in pyproject.toml
## License
This code is licensed under CC BY-NC-SA 4.0. See the original AlphaFold 3 repository for more details on usage restrictions and licensing terms.
## Citation
If you use this code in your research, please cite the AlphaFold 3 paper:
```
Abramson, J., Adler, J., Dunger, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630, 493�?00 (2024).
```
## Links
- [Original AlphaFold 3 Repository](https://github.com/google-deepmind/alphafold3)
- [AlphaFold 3 Paper](https://www.nature.com/articles/s41586-024-07487-w)
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