Table 3.
List of AI-based software for drug discovery, development, and analysis.
| Reference | Description | Source code |
|---|---|---|
| AlphaFold2 [35] | Deep learning based model for 3D structure prediction of proteins from amino acid sequences | https://github.com/deepmind/alphafold/ |
| DeepChem [80] | A deep learning library for drug discovery and computational chemistry | https://github.com/deepchem/deepchem |
| DeepBind [81] | A computational tool to analyze binding between the protein and DNA/RNA | https://github.com/MedChaabane/DeepBind-with-PyTorch |
| DeepBar [82] | A method for accurate and fast prediction of binding free energy | https://fastmbar.readthedocs.io/en/latest/ |
| Deep-Screening [83] | Web-server based in deep learning for virtual screening of compounds | http://deepscreening.xielab.net/ |
| DeepScreen [84] | High performance drug target interaction | https://github.com/cansyl/DEEPScreen |
| DeepConv-DTI [45] | A convolutional neural network based model for predicting drug-target interactions | https://github.com/GIST-CSBL/DeepConv-DTI |
| DeepPurpose [24] | A Deep learning library for drug-target interaction, drug-drug interaction, protein-protein interaction and protein function prediction | https://github.com/kexinhuang12345/DeepPurpose |
| DeepTox [85] | A deep learning model for toxicity prediction of chemical compounds | http://www.bioinf.jku.at/research/DeepTox/ |
| AtomNet [86] | A deep convolutional neural network for bioactivity prediction | github |
| PathDSP [87] | A deep learning method for predicting drug sensitivity using cancer cell lines | https://github.com/TangYiChing/PathDSP |
| Graph level representation [88] | Learning graph representation for drug discovery | https://github.com/ZJULearning/graph_level_drug_discovery |
| Chemical VAE [89] | An auto-encoder based framework to generate new molecules | https://github.com/aspuru-guzik-group/chemical_vae/ |
| DeepGraphMol [87] | A computational method for molecule generation with desired properties using graph neural networks and reinforcement learning | https://github.com/dbkgroup/prop_gen |
| TorchDrug [26] | A pytorch based flexible framework for drug discovery models | https://torchdrug.ai/ |