Protein Function Annotations in Three Ways

About

Do my novel chemical compounds and/or proteomics method...

1. enrich a set of particular structural domains and functional pathways?
2. access a new "druggable" space?
3. target important classes of "undruggable" proteins?

Set Up

1. Particular modules necessary to run each script or notebook are listed in the setup section of each README.
2. Input files <compiled_proteins.csv> are required and can be obtained from the MS-CpDAA Analysis Suite.
3. Additional files listing specific UniProtKB accession identifiers can also be utilized as input.
4. UniProtKB files and Human Protein Atlas files need to be downloaded with the provided links and required columns listed in each individual setup section.
5. Additional input files are provided in the accompanying data folders.

Usage

1. Custom gene set enrichment
2. Protein druggability annotations
3. Protein function classifications

Citation

1. Boatner LM, Palafox MF, Schweppe DK, Backus KM. CysDB: a human cysteine database based on experimental quantitative chemoproteomics. Cell Chem Biol. 2023 Jun 15;30(6):683-698.e3. doi: 10.1016/j.chembiol.2023.04.004. Epub 2023 Apr 28. PMID: 37119813; PMCID: PMC10510411.
2. Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol. 2023 Jul 20;30(7):811-827.e7. doi: 10.1016/j.chembiol.2023.06.008. Epub 2023 Jul 6. PMID: 37419112; PMCID: PMC10510412.
3. Takechi S, Ngo C, Burton N, Villanueva M, Boatner L, Yu F, Kim P, Biletch E, Turmon A, Nesvizhskii A, Backus, K. Silyl Ether Enables High Coverage Chemoproteomic Interaction Site Mapping. ChemRxiv. 2024 Jun 10.