awesome-DrugAI

A comprehensive list of drug AI (AI-aided de novo drug discovery) papers and materials. Will be frequently updated.

Table of Contents

• Main Applications

• Papers (Topic-wise, Reverse Chronological Order))

  • Virtual screening & Docking & Molecular interaction
  • Molecular dynamics
  • ADMET prediction
  • Protein property prediction
  • Protein structure prediction
  • Protein design
  • Retrosynthetic analysis
  • Generative chemistry
  • Drug repurposing
  • Antibiotic discovery

• Tutorials & Talks & Blogs

• Open Source Libraries & Platforms

Main Applications

• [ ] Virtual screening
• [ ] Protein structure prediction
• [ ] Retrosynthetic analysis
• [ ] Generative chemistry
• [ ] ADMET prediction
• [ ] Drug repurposing

Papers (Topic-wise, Reverse Chronological Order)

Virtual screening & Docking & Molecular interaction

• [ ] Ganea, O. E., Huang, X., Bunne, C., Bian, Y., Barzilay, R., Jaakkola, T., & Krause, A. (2021).
  Independent SE (3)-Equivariant Models for End-to-End Rigid Protein Docking. arXiv preprint arXiv:2111.07786.

Molecular dynamics

ADMET prediction

• [ ] Rong, Y., Bian, Y., Xu, T., Xie, W., Wei, Y., Huang, W., & Huang, J. (2020).
  Self-supervised graph transformer on large-scale molecular data. NeurIPS 2020.

Protein property prediction

Protein structure prediction

• [ ] Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., ... & Hassabis, D. (2021).
  Highly accurate protein structure prediction with AlphaFold. Nature, 1-11.

• [ ] Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., ... & Baker, D. (2021).
  Accurate prediction of protein structures and interactions using a 3-track network. Science.

Protein design

Retrosynthetic analysis

Generative chemistry

• [ ] Shi, C., Luo, S., Xu, M., & Tang, J. (2021).
  Learning gradient fields for molecular conformation generation. arXiv preprint arXiv:2105.03902.

• [ ] Shi, C., Xu, M., Zhu, Z., Zhang, W., Zhang, M., & Tang, J. (2020).
  Graphaf: a flow-based autoregressive model for molecular graph generation. arXiv preprint arXiv:2001.09382.

Drug repurposing

• [ ] Pushpakom, S., Iorio, F., Eyers, P. A., Escott, K. J., Hopper, S., Wells, A., ... & Pirmohamed, M. (2019).
  Drug repurposing: progress, challenges and recommendations. Nature reviews Drug discovery, 18(1), 41-58.

Antibiotic discovery

• [ ] Stokes, J. M., Yang, K., Swanson, K., Jin, W., Cubillos-Ruiz, A., Donghia, N. M., ... & Collins, J. J. (2020).
  A deep learning approach to antibiotic discovery. Cell, 180(4), 688-702.

Tutorials & Talks & Blogs

• [ ] Jian Tang, Fei Wang, Feixiong Cheng. (2021).
  AAAI 2021 Tutorial Artificial Intelligence for Drug Discovery

Open Source Libraries & Platforms

• [ ] Tencent Holdings Ltd. (2020).
  The iDrug platform.