An experimental project for mapping proteomic data onto 3D protein structures in Jupyter Notebooks.
Post-translational modifications (PTMs) modulate protein function. By mapping the locations of modified amino acid residues onto 3D protein structures, insights into the effect of PTMs can be obtained.
Example: Oxidated cysteines highlighted in a 3D protein structure.
| Notebook | Description | Data Source |
|---|---|---|
| QueryPdbPTM.ipynb | Query and visualize PTMs present in PDB structures. | BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Gao J, Prlić A, Bi C Bluhm WF, Dimitropoulos D, Xu D Bourne, PE, Rose PW, Bioinformatics (2017) 33: 2047–2049. doi: doi.org/10.1093/bioinformatics/btx101 |
| QueryDbPTM.ipynb | Query and visualize PTMs from the dbPTM database. | dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Huang KY, Su MG, Kao HJ, Hsieh YC, Jhong JH, Cheng KH, Huang HD, Lee TY, Nucleic Acids Res. (2016) 44(D1):D435-46. doi: doi.org/10.1093/bioinformatics/btx101 |
| BrowseDbPTM.ipynb | Browse and visualize PTMs from the dbPTM database by type of PTM. | dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. Huang KY, Su MG, Kao HJ, Hsieh YC, Jhong JH, Cheng KH, Huang HD, Lee TY, Nucleic Acids Res. (2016) 44(D1):D435-46. doi: doi.org/10.1093/bioinformatics/btx101 |
| CysOxidationInPDB.ipynb | Find and visualize oxidized forms of L-cysteine in the PDB. | BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank. Gao J, Prlić A, Bi C Bluhm WF, Dimitropoulos D, Xu D Bourne, PE, Rose PW, Bioinformatics (2017) 33: 2047–2049. doi:doi.org/10.1093/bioinformatics/btx101 |
| CysOxidationTo 3DStructure.ipynb |
Map and visualize cysteine oxidations for the proteomics study by Akter et al. | Chemical proteomics reveals new targets of cysteine sulfinic acid reductase. Akter S, Fu L, Jung Y, Conte ML, Lawson JR, Lowther WT, Sun, Liu, Yang J, Carroll KS, Nat Chem Biol. (2018) Sep 3. doi: 10.1038/s41589-018-0116-2 |
| CysOxidationProteomicAnd StructuralEvidence.ipynb |
Find and visualize 3D structural evidence for the proteomics study by Akter et al. | Chemical proteomics reveals new targets of cysteine sulfinic acid reductase. Akter S, Fu L, Jung Y, Conte ML, Lawson JR, Lowther WT, Sun, Liu, Yang J, Carroll KS, Nat Chem Biol. (2018) Sep 3. doi: 10.1038/s41589-018-0116-2 |
| PTMsigDbTo 3DStructure.ipynb |
Map and visualize phosphorylation sites from PTMsigDB, a collection of modification site-specific signatures of perturbations, kinase activities and signaling pathways. | A Curated Resource for Phosphosite-specific Signature Analysis. Krug K, Mertins P, Zhang B, Hornbeck P, Raju R, Ahmad R, Szucs M, Mundt F, Forestier D, Jane-Valbuena J, Keshishian H, Gillette MA, Tamayo P, Mesirov JP, Jaffe JD, Carr SA and Mani DR, Molecular & Cellular Proteomics (2019). doi: 10.1074/mcp.TIR118.000943 |
| S-SulphenylationTo 3DStructure.ipynb |
Map and visualize S-sulphenylations sites. | Diverse Redoxome Reactivity Profiles of Carbon Nucleophiles. Gupta V, Yang J, Liebler DC, Carroll KS, J Am Chem Soc. (2017) 139(15):5588-5595. doi: 10.1021/jacs.7b01791 |
The Jupyter Notebooks in this repository can be run in your web browser using two freely available servers: CyVerse/VICE and Binder. Click on the launch buttons below to launch Jupyter Lab. It may take several minutes for Jupyter Lab to launch.
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Follow these step to run Jupyter Lab on VICE
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Interested in a collaboration? Please send us use cases.
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Goff, Stephen A., et al. (2011) The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Frontiers in Plant Science 2. doi: 10.3389/fpls.2011.00034
Project Jupyter, et al. (2018) Binder 2.0 - Reproducible, Interactive, Sharable Environments for Science at Scale. Proceedings of the 17th Python in Science Conference. 2018. doi: 10.25080/Majora-4af1f417-011
Rego N, Koes, D (2015) 3Dmol.js: molecular visualization with WebGL, Bioinformatics 31, 1322–1324. doi: 10.1093/bioinformatics/btu829
The MMTF project (Compressive Structural BioInformatics: High Efficiency 3D Structure Compression) is supported by the National Cancer Institute of the National Institutes of Health under Award Number U01CA198942. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
The CyVerse project is supported by the National Science Foundation under Award Numbers DBI-0735191, DBI-1265383, and DBI-1743442. URL: www.cyverse.org