Chiralpedia

Databases

• Gaulton A, Hersey A, Nowotka M, et al. The ChEMBL database in 2017. Nucleic Acids Res. 2017;45(D1):D945-D954.
  doi:10.1093/nar/gkw1074.
• Kim S, Chen J, Cheng T, et al. PubChem in 2023: New data content and improved web interfaces. Nucleic Acids Res. 2023;51(D1):D1373-D1380.
  doi:10.1093/nar/gkac956.
• Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28(1):235-242.
  doi:10.1093/nar/28.1.235.

Molecular Representations

• Weininger D. SMILES, a chemical language and information system. I. Introduction to methodology and encoding rules. J Chem Inf Comput Sci. 1988;28(1):31-36.
  doi:10.1021/ci00057a005.
• Krenn M, Häse F, Nigam A, Friederich P, Aspuru-Guzik A. SELFIES: A robust representation of semantically constrained graphs with an example application in chemistry. Mach Learn Sci Technol. 2020;1:045024.
  doi:10.1088/2632-2153/aba947.

Open-Source Software & Platforms

• RDKit. Open-source cheminformatics software. Available at: https://www.rdkit.org
• DeepChem. Open-source deep learning framework for drug discovery. Available at: https://deepchem.io
• ChemBERTa. Large-scale self-supervised molecular language model. Available at: https://arxiv.org/abs/2010.09885
• PyTorch Geometric. Graph neural network library. Available at: https://pytorch-geometric.readthedocs.io
• DGL-LifeSci. Deep Graph Library for life sciences. Available at: https://lifesci.dgl.ai