📖 Table of contents
- De novo protein prediction and design
- De novo fragment design
- Databases and Datasets
- Cookbooks
- Blogs
💡 Notes
- Personal notes to keep track of new tools and methodologies related to computer-aided drug design.
De novo protein prediction and design
- fsacdallago/folding_tools
- duerrsimon/folding_tools
- Peldom/papers_for_protein_design_using_DL
- yjcyxky/A Collection of Platform, Tools, Resources and Companies for Antibody Engineering
- yangkky/Machine-learning-for-proteins
- Kuhlman-Lab
- Oxford Protein Informatics Group
- AspirinCode/papers-for-molecular-design-using-DL
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.
Cookbooks
- Deep Learning for Molecules and Materials Book by Andrew White
- labml.ai Annotated Pytorch Paper Implementations
- OpenMM Cookbook