Molecule Transformers Generator

This folder contains Molecule Transformer Generator (MGT), i.e., a collection of scripts to generate new molecules using a simple transformer architecture in Python. The work is based on the publications [1] and [2].

Installation

To work with the repository, one can simply clone it in the local machine:

git clone https://github.com/andreabellome/molecule_transfromer_generator.git

If one wants to specify a specific target directory (should be empty):

git clone https://github.com/andreabellome/molecule_transfromer_generator.git /path/to/your/target/directory

where /path/to/your/target/directory should be replaced with the desired local taregt directory.

The main requirements is to use a Python version that is 3.10, since Tensorflow is employed.

All the other requirements can be downloaded using:

pip install -r requirements.txt

Please use the script joudiciously as it might take high computational effort.

License & Contributors

The work is under license CC BY-NC-SA 4.0, that is an Attribution Non-Commercial license. One can find the specifics in the LICENSE file.

Only invited developers can contribute to this repository. Current active contributors are:

• Lorenzo Graziani
• Andrea Bellome

References

[1] Horne, R.I., Andrzejewska, E.A., Alam, P. et al. Discovery of potent inhibitors of α-synuclein aggregation using structure-based iterative learning. Nat Chem Biol 20, 634–645 (2024). https://doi.org/10.1038/s41589-024-01580-x

[2] Mazuz, E., Shtar, G., Shapira, B. et al. Molecule generation using transformers and policy gradient reinforcement learning. Sci Rep 13, 8799 (2023). https://doi.org/10.1038/s41598-023-35648-w