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Phosphoproteomics

License

This repository covers some bioinformatics analysis applied to phosphoproteomics study.


Ras GTPase-activating protein-binding protein 2 (G3BP2) predicted by AlphaFold2. This protein has several ubiquitination sites annotated in PhosphoSitePlus.

Instalation dependencies

Install dependencies with mamba

mamba create --name phosphoproteomics python=3 pandas matplotlib numpy biopython plotly pypdb

Notebooks

Useful databases for PTM analysis

  • dbPTM: an integrated resource for protein post-translational modifications (PTMs).
  • disprot: database of intrinsically disordered proteins.
  • MobiDB: a database of protein disorder and mobility annotations.
  • Ochoa, D., Jarnuczak, A.F., Viéitez, C. et al. The functional landscape of the human phosphoproteome. Nat Biotechnol 38, 365–373 (2020). https://doi.org/10.1038/s41587-019-0344-3
  • Phospho.ELM: a database of S/T/Y phosphorylation sites.
  • PhosphoSitePlus: information and tools for the study of protein post-translational modifications (PTMs)
  • ProteomeScout: database of proteins and post-translational modifications.
  • PTMcode 2: known and predicted functional associations between protein post-translational modifications (PTMs).
  • Qoukka: webserver for prediction of kinase family-specific phosphorylation sites.
  • Uniprot: comprehensive, high-quality and freely accessible resource of protein sequence and functional information

Author

Fernando Pozo - @fpozoca - Google Scholar[email protected] - github.com/fpozoc

License

See LICENSE file.