SS-1: Potential New Biobricks - Githubissues

biobricks-ai / biobricks

BioBricks makes loading data from biological datasets and databases easy. Python and R interfaces, data version control, and an API for pulling datasets that have been converted to easy-to-use formats.

https://docs.biobricks.ai

MIT License

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SS-1: Potential New Biobricks #38

Open Sulstice opened 1 month ago

Sulstice commented 1 month ago

Hi,

Suggestions for new additions:

1. MHCFlurry for perhaps being a potential brick for MHC 1 class proteins binding affinity.

2. Binding MOAD (mother of all data)

Paper: Hu, L., Benson, M. L., Smith, R. D., Lerner, M. G. & Carlson, H. A. Binding moad (mother of all databases). Proteins: Structure, Function, and Bioinformatics 60, 333–340 (2005).

3. D3R Drug Design Data Resource (For All Kinases)

Data Link: https://drugdesigndata.org/about/sources

4. NIDDK data repository: a central collection of clinical trial data

https://pubmed.ncbi.nlm.nih.gov/16595012/

5. KIBA Dataset: Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis

Paper: https://pubs.acs.org/doi/10.1021/ci400709d

6. Comprehensive analysis of kinase inhibitor selectivity

Paper: https://www.nature.com/articles/nbt.1990

7. DUDE: Database of Useful Decoys.

Data Link: https://dude.docking.org/
Paper: https://pubs.acs.org/doi/10.1021/jm300687e

zmughal commented 1 month ago

drugbank-open-data: https://go.drugbank.com/releases/latest#open-data

These are also in PubChem via the PubChem-KG and PubChem annotations, but might be useful to go to the original source.