Create README.md
#2
by
reach-vb
HF staff
- opened
README.md
ADDED
@@ -0,0 +1,63 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
1 |
+
<h1 align="center">Boltz-1:
|
2 |
+
|
3 |
+
Democratizing Biomolecular Interaction Modeling
|
4 |
+
</h1>
|
5 |
+
|
6 |
+
Boltz-1 is an open-source model which predicts the 3D structure of proteins, rna, dna and small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues.
|
7 |
+
|
8 |
+
For more information about the model, see our [technical report](https://gcorso.github.io/assets/boltz1.pdf).
|
9 |
+
|
10 |
+
## Installation
|
11 |
+
Install boltz with PyPI (recommended):
|
12 |
+
|
13 |
+
```
|
14 |
+
pip install boltz
|
15 |
+
```
|
16 |
+
|
17 |
+
or directly from GitHub for daily updates:
|
18 |
+
|
19 |
+
```
|
20 |
+
git clone https://github.com/jwohlwend/boltz.git
|
21 |
+
cd boltz; pip install -e .
|
22 |
+
```
|
23 |
+
> Note: we recommend installing boltz in a fresh python environment
|
24 |
+
|
25 |
+
## Inference
|
26 |
+
|
27 |
+
You can run inference using Boltz-1 with:
|
28 |
+
|
29 |
+
```
|
30 |
+
boltz predict input_path
|
31 |
+
```
|
32 |
+
|
33 |
+
Boltz currently accepts three input formats:
|
34 |
+
|
35 |
+
1. Fasta file, for most use cases
|
36 |
+
|
37 |
+
2. A comprehensive YAML schema, for more complex use cases
|
38 |
+
|
39 |
+
3. A directory containing files of the above formats, for batched processing
|
40 |
+
|
41 |
+
To see all available options: `boltz predict --help` and for more informaton on these input formats, see our [prediction instructions](docs/prediction.md).
|
42 |
+
|
43 |
+
## Training
|
44 |
+
|
45 |
+
If you're interested in retraining the model, see our [training instructions](docs/training.md).
|
46 |
+
|
47 |
+
## Contributing
|
48 |
+
|
49 |
+
We welcome external contributions and are eager to engage with the community. Connect with us on our [Slack channel](https://boltz-community.slack.com/archives/C0818M6DWH2) to discuss advancements, share insights, and foster collaboration around Boltz-1.
|
50 |
+
|
51 |
+
## Coming very soon
|
52 |
+
|
53 |
+
- [ ] Pocket conditioning support
|
54 |
+
- [ ] More examples
|
55 |
+
- [ ] Full data processing pipeline
|
56 |
+
- [ ] Colab notebook for inference
|
57 |
+
- [ ] Confidence model checkpoint
|
58 |
+
- [ ] Support for custom paired MSA
|
59 |
+
- [ ] Kernel integration
|
60 |
+
|
61 |
+
## License
|
62 |
+
|
63 |
+
Our model and code are released under MIT License, and can be freely used for both academic and commercial purposes.
|