Added inference for Boltz-1 using Colab

README.md

@@ -5,6 +5,13 @@ Democratizing Biomolecular Interaction Modeling
 
 ![](docs/boltz1_pred_figure.png)
 
+Boltz-1 is an open-source model which predicts the 3D structure of proteins, RNA, DNA an<h1 align="center">Boltz-1:
+
+Democratizing Biomolecular Interaction Modeling
+</h1>
+
+![](docs/boltz1_pred_figure.png)
+
 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. 
 
 For more information about the model, see our [technical report](https://gcorso.github.io/assets/boltz1.pdf).
@@ -24,6 +31,97 @@ cd boltz; pip install -e .
 ```
 > Note: we recommend installing boltz in a fresh python environment
 
+## Inference on Colab
+
+You can run inference using the Boltz-1 model directly in Google Colab. Click the link below to open the notebook:
+
+[Google Colab](https://colab.research.google.com/drive/1B_xSLii8ZMvp4K4XL2zslQVbKIjWV-mp?usp=sharing)
+
+## Inference
+
+You can run inference using Boltz-1 with:
+
+```
+boltz predict input_path
+```
+
+Boltz currently accepts three input formats:
+
+1. Fasta file, for most use cases
+
+2. A comprehensive YAML schema, for more complex use cases
+
+3. A directory containing files of the above formats, for batched processing
+
+To see all available options: `boltz predict --help` and for more informaton on these input formats, see our [prediction instructions](docs/prediction.md).
+
+## Training
+
+If you're interested in retraining the model, see our [training instructions](docs/training.md).
+
+## Contributing
+
+We welcome external contributions and are eager to engage with the community. Connect with us on our [Slack channel](https://join.slack.com/t/boltz-community/shared_invite/zt-2uexwkemv-Tqt9E747hVkE0VOWlgOcIw) to discuss advancements, share insights, and foster collaboration around Boltz-1.
+
+## Coming very soon
+
+- [x] Auto-generated MSAs using MMseqs2
+- [x] More examples
+- [ ] Support for custom paired MSA
+- [ ] Confidence model checkpoint
+- [ ] Pocket conditioning support
+- [ ] Full data processing pipeline
+- [x] Colab notebook for inference
+- [ ] Kernel integration
+
+## License
+
+Our model and code are released under MIT License, and can be freely used for both academic and commercial purposes.
+
+
+## Cite
+
+If you use this code or the models in your research, please cite the following paper:
+
+```bibtex
+@article{wohlwend2024boltz1,
+  author = {Wohlwend, Jeremy and Corso, Gabriele and Passaro, Saro and Reveiz, Mateo and Leidal, Ken and Swiderski, Wojtek and Portnoi, Tally and Chinn, Itamar and Silterra, Jacob and Jaakkola, Tommi and Barzilay, Regina},
+  title = {Boltz-1: Democratizing Biomolecular Interaction Modeling},
+  year = {2024},
+  doi = {10.1101/2024.11.19.624167},
+  journal = {bioRxiv}
+}
+```
+
+In addition if you use the automatic MSA generation, please cite:
+
+```bibtex
+@article{mirdita2022colabfold,
+  title={ColabFold: making protein folding accessible to all},
+  author={Mirdita, Milot and Sch{\"u}tze, Konstantin and Moriwaki, Yoshitaka and Heo, Lim and Ovchinnikov, Sergey and Steinegger, Martin},
+  journal={Nature methods},
+  year={2022},
+}
+```
+d small molecules; it handles modified residues, covalent ligands and glycans, as well as condition the generation on pocket residues. 
+
+For more information about the model, see our [technical report](https://gcorso.github.io/assets/boltz1.pdf).
+
+## Installation
+Install boltz with PyPI (recommended):
+
+```
+pip install boltz
+```
+
+or directly from GitHub for daily updates:
+
+```
+git clone https://github.com/jwohlwend/boltz.git
+cd boltz; pip install -e .
+```
+> Note: we recommend installing boltz in a fresh python environment
+
 ## Inference
 
 You can run inference using Boltz-1 with:
@@ -58,7 +156,7 @@ We welcome external contributions and are eager to engage with the community. Co
 - [ ] Confidence model checkpoint
 - [ ] Pocket conditioning support
 - [ ] Full data processing pipeline
-- [ ] Colab notebook for inference
+- [x] Colab notebook for inference
 - [ ] Kernel integration
 
 ## License