Drug Design Hub

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Resources ​

Curated tools, datasets, and references for drug discovery.

Computational Tools ​

Cheminformatics ​

  • RDKit - Open-source cheminformatics toolkit for molecule manipulation and property calculation
  • Open Babel - Chemical toolbox for file format conversion and molecular property analysis
  • ChemAxon - Commercial suite for cheminformatics and drug discovery

Molecular Docking ​

  • AutoDock Vina - Fast and accurate molecular docking program
  • DOCK - Suite for molecular docking and virtual screening
  • Glide - High-precision ligand-receptor docking (Schrödinger)

Molecular Dynamics ​

  • GROMACS - High-performance molecular dynamics package
  • AMBER - Comprehensive molecular dynamics simulation suite
  • OpenMM - Toolkit for molecular simulation with GPU acceleration
  • NAMD - Parallel molecular dynamics code for large biomolecular systems

Machine Learning for Drug Discovery ​

  • DeepChem - Python library for deep learning in chemistry and biology
  • PyTorch Geometric - Graph neural networks for molecular modeling
  • Chemprop - Message passing neural networks for molecular property prediction
  • TorchDrug - Machine learning platform for drug discovery

Visualization ​

  • PyMOL - Molecular visualization system for 3D structures
  • VMD - Visual Molecular Dynamics for displaying and analyzing molecular systems
  • Chimera / ChimeraX - Interactive visualization and analysis of molecular structures

Databases ​

Chemical Compounds ​

  • PubChem - Free chemistry database with millions of compounds
  • ChEMBL - Database of bioactive molecules with drug-like properties
  • ZINC - Free database of commercially available compounds for virtual screening
  • DrugBank - Comprehensive resource combining drug data with target information

Protein Structures ​

  • Protein Data Bank (PDB) - Repository of 3D structural data of proteins and nucleic acids
  • AlphaFold DB - Database of protein structure predictions by AlphaFold
  • UniProt - Comprehensive protein sequence and functional information database

Molecular Interactions ​

  • BindingDB - Database of measured binding affinities for protein-ligand complexes
  • PDBbind - Collection of binding affinity data for protein-ligand complexes
  • STITCH - Database of protein-chemical interactions

Pharmacology & Toxicity ​

  • ADMET Predictor - Software for predicting ADMET properties
  • Tox21 - Database of toxicity data for chemical compounds
  • SuperTarget - Database of drug-target relationships

Learning Resources ​

Online Courses ​

Books ​

  • "Drug Design: Structure- and Ligand-Based Approaches" by Kenneth M. Merz Jr. et al.
  • "Introduction to Computational Chemistry" by Frank Jensen
  • "Molecular Modelling: Principles and Applications" by Andrew R. Leach
  • "Deep Learning for the Life Sciences" by Bharath Ramsundar et al.

Tutorials & Guides ​

Research Papers & Reviews ​

Foundational Papers ​

  • Lipinski et al. (1997) - "Rule of Five" for drug-likeness
  • Shoichet (2004) - Virtual screening of chemical libraries
  • Senior et al. (2020) - AlphaFold: Improved protein structure prediction

Recent Reviews ​

  • Schneider (2018) - Automating drug discovery
  • Stokes et al. (2020) - Deep learning for antibiotic discovery
  • Jumper et al. (2021) - Highly accurate protein structure prediction with AlphaFold

Community & Forums ​

Contributing ​

Have a tool, dataset, or resource to add? This page is continuously updated with valuable resources for the drug discovery community. Feel free to suggest additions through our repository.

Last updated: January 2025