
Ligand binding affinity prediction using deep learning - bergos
https://www.bergnet.org/2017/02/ligand-binding-deep-learning/
======
bergos
I've implemented ligand binding affinity prediction using deep learning and
also wrote a blog post about it. The post doesn't cover only the technical
stuff, but also a little bit the history of the idea. It uses SMILES token to
feed the neural network with the molecule structures. I'm using alternative
representations for data augmentation, which wasn't used by similar projects
before. The training is done with Keras Gaia, which was developed for this
project. It simplifies the training process for different models and datasets.
The SPARQL wrapper for BindingDB could be of interest for anyone who would
like to fetch BindingDB data using ChEMBL queries. I also implemented a SMILES
parser in JavaScript, because there wasn't any implementation available.

