Phosphoproteomics

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.

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• Phosphoproteomics
• Instalation dependencies
• Notebooks
• Useful databases for PTM analysis
• Author
• License

Instalation dependencies

Install dependencies with mamba

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

Notebooks

• 01_file-processing.ipynb: File processing.
• 02_structural-characterization.ipynb: Structural characterization of phosphorylation sites: analysis of the region, secondary structure and accessibility of the phospho-S/T/Y peptides.
• 03_motif-analysis.ipynb: Phosphorylation motif analysis classification.
• 04_biochemical-properties-analysis.ipynb: Are the phospho-peptides: Acidic-, basic-,proline-,asparagine-, or hydrophobic-directed?
• 05_clustering-analysis.ipynb: PTM clusters analysis.
• 06_motifX.ipynb: Identification of new motifs with MotifX.

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.