hERG_toxicity

Machine learning models to predict hERG-related toxicity of molecules

Dataset

The description of the dataset can be found here: Siramshetty et al., 2020. Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the ‘Big Data’ Era.

source of code: https://github.com/ncats/herg-ml.git

Preprocessing - Morgan fingerprints

https://deepnote.com/workspace/hana-svachova-e5fcfdb8-3686-46a9-a57a-2ff47776e57f/project/TheMama2022preprocess1-0e7676dc-6723-4d27-b8a2-de62b19a9e87/%2FGetting%20started.ipynb

source of code: https://youtube.com/playlist?list=PLNrPuOfDng-GDtCjGs1UFbZaNRfSY8jUW

SVM

https://deepnote.com/workspace/hana-svachova-e5fcfdb8-3686-46a9-a57a-2ff47776e57f/project/TheMama2022SVM2-ec408c20-d29e-4ef9-b475-8b29e2f62a2e/%2FGetting%20started.ipynb

source of code: https://www.kaggle.com/code/prashant111/svm-classifier-tutorial/notebook

Decision tree

https://deepnote.com/workspace/hana-svachova-e5fcfdb8-3686-46a9-a57a-2ff47776e57f/project/TheMama2022Decisiontree3-a99193e4-6af1-45d9-b602-8d663932099a/%2FGetting%20started.ipynb

source of code: https://www.kaggle.com/code/prashant111/decision-tree-classifier-tutorial

DNN

https://deepnote.com/workspace/hana-svachova-e5fcfdb8-3686-46a9-a57a-2ff47776e57f/project/TheMama2022DNN4-9e73c609-5701-4d12-a1dd-e95ca51974b7/%2FGetting%20started.ipynb

source of code: https://github.com/ncats/herg-ml.git

References

Webel et al., 2020, Revealing cytotoxic substructures in molecules using deep learning, Journal of Computer-Aided Molecular Design volume 34, p 731–746