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📖 Table of contents

💡 Notes

  • Personal notes to keep track of new tools and methodologies related to computer-aided drug design.

De novo protein prediction and design


Denovo fragment design

  • AutoFragDiff
  • FEGrow
  • DiffLinker

Databases and Datasets

  • Therapeutics Data Commons
    • Therapeutics Data Commons is a coordinated initiative to access and evaluate artificial intelligence capability across therapeutic modalities and stages of discovery. The Commons is a resource with AI-solvable tasks, AI-ready datasets, and curated benchmarks, providing an ecosystem of tools, libraries, leaderboards, and community resources, including data functions, strategies for systematic model evaluation, meaningful data splits, data processors, and molecule generation oracles.
  • ProTherm
    • ProThermDB, thermodynamic Database for Proteins and Mutants (ProThermDB) contains more than 32,000 data of several thermodynamic parameters such as melting temperature, free energy obtained with thermal and denaturant denaturation, enthalpy change, and heat capacity change along with experimental methods and conditions, sequence, structure, and literature information.

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