Scop3P-notebooks

Jupyter Notebook examples of Scop3P REST API services as well as ShinyApp/Voilà applications for the Scop3P-Toolkit.

Published container

This repository publishes the Galaxy-facing bio2byte/scop3p-toolkit container. The image packages the single-container portal exposed on port 8000 and is the intended entrypoint for a UseGalaxy interactive tool.

• Docker image: bio2byte/scop3p-toolkit
• Dockerfile target: scop3p-toolkit
• App-specific documentation: apps/README.md

Build and run the toolkit image

Build the published image locally:

DOCKER_DEFAULT_PLATFORM=linux/amd64 docker build \
  -f docker/Dockerfile \
  -t bio2byte/scop3p-toolkit:local \
  .

Run it locally:

docker run --rm -p 8000:8000 bio2byte/scop3p-toolkit:local

Then open http://localhost:8000 to access the toolkit selector and launch the bundled interactive apps.

Continuous delivery to Docker Hub

The GitHub Actions workflow lives in docker-publish.yml and has two stages:

1. Pytest suite Runs on pull requests, manual workflow dispatches, and version-tag pushes. It installs the Python dependencies from requirements-biophysics.txt and requirements-shiny.txt, then runs:

   pytest tests/unit tests/integration

2. Build and publish Docker image Runs only after the tests pass.

   • On pull requests and workflow_dispatch runs:
     • builds the scop3p-toolkit target for linux/amd64
     • validates that the Docker image can be built
     • does not publish anything to Docker Hub
   • On version tags matching v*:
     • builds the same image target
     • logs in to Docker Hub
     • publishes these tags:
       • latest
       • sha-<short-commit>
       • <git-tag> such as v1.2.3

The workflow resolves the Docker repository namespace in this order:

1. DOCKERHUB_NAMESPACE repository variable
2. DOCKERHUB_USERNAME repository secret
3. the lowercased GitHub repository owner as a fallback for build-only runs

Required repository secrets:

• DOCKERHUB_USERNAME
• DOCKERHUB_TOKEN

Optional repository variable:

• DOCKERHUB_NAMESPACE

If DOCKERHUB_NAMESPACE is not set, the workflow publishes to the same namespace as DOCKERHUB_USERNAME.

About Scop3P¹

Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context

Protein phosphorylation is a key post-translational modification in many biological processes and is associated to human diseases such as cancer and metabolic disorders. The accurate identification, annotation, and functional analysis of phosphosites are therefore crucial to understand their various roles. Phosphosites are mainly analyzed through phosphoproteomics, which has led to increasing amounts of publicly available phosphoproteomics data. Several resources have been built around the resulting phosphosite information, but these are usually restricted to the protein sequence and basic site metadata. What is often missing from these resources, however, is context, including protein structure mapping, experimental provenance information, and biophysical predictions. We therefore developed Scop3P: a comprehensive database of human phosphosites within their full context. Scop3P integrates sequences (UniProtKB/Swiss-Prot), structures (PDB), and uniformly reprocessed phosphoproteomics data (PRIDE) to annotate all known human phosphosites. Furthermore, these sites are put into biophysical context by annotating each phosphoprotein with per-residue structural propensity, solvent accessibility, disordered probability, and early folding information. Scop3P, available at https://iomics.ugent.be/scop3p, presents a unique resource for visualization and analysis of phosphosites and for understanding of phosphosite structure–function relationships.

HTTP REST API

Open the Scop3P API using the Swagger UI click here

Jupyter Notebook index

This section contains the links to our online Jupyter Notebooks. We would like to invite you to contribute to our repository if you want to share your Jupyter Notebooks related to Scop3P. Please contact us at pathmanaban.ramasamy@ugent.be.

Modifications endpoint (GET scop3p/api/modifications)

This notebook fetches PTMs and metadata for a given UniProt ID from Scop3P modification endpoint and visualizes them using simple plots.

Click on the next link to open the Jupyter Notebook in an executable environment:

Structural and biophysical visualization framework

This notebook enables interactive visualization of PTMs and disease variants by integrating Scop3P and UniProt data with 3D structural mapping onto PDB and AlphaFold models. It supports biophysical property prediction, residue interaction network (RIN) analysis, and structural alignment to explore PTM-driven structural and functional effects.

Integrated structural and biophysical visualization of PTMs and disease variants

Click on the next link to open the Jupyter Notebook in an executable environment:

Notebook (JupyterLab)	Interactive app (Voilà)

If there is any launch error then please open the Notebook (JupyterLab) link first to authenticate,
then launch the Interactive app (Voilà).

Biophysical prediction and mutation effects

This notebook predicts sequence-based biophysical properties of proteins from a UniProt ID and visualizes them using interactive plots. Users can introduce one or multiple amino-acid mutations, re-compute the predictions on the mutated sequence, and directly compare wild-type and mutant profiles. A final inference step summarizes the impact of mutations based on changes in predicted biophysical properties.Simple notebook fetching modifications for UniProt ID O00571 (O00571 · DDX3X_HUMAN), predicting the biophysical properties and visualizing the results using different strategies.

Predicted biophysical profiles of wild-type and mutant protein sequences, highlighting phosphorylation sites along the 1D amino-acid coordinate

Click on the next link to open the Jupyter Notebook in an executable environment:

Notebook (JupyterLab)	Interactive app (Voilà)

Peptide-to-structure mapping

Interactive mapping of phosphopeptides—either fetched from Scop3P or uploaded by the user onto AlphaFold structures to visualize peptide coverage and modification sites.

Mapping phosphopeptides onto protein structures

Click on the next link to open the Jupyter Notebook in an executable environment:

Workflow	Notebook (JupyterLab)	Interactive app (Voilà)
Scop3P peptides
Upload your own peptides

About

The repository was created by the Bio2Byte research group at Vrije Universiteit Brussel and is maintained in collaboration with Compomics at the VIB-UGent Center for Medical Biotechnology.

• Compomics: Computational Omics and Systems Biology Group
• IBsquare: The Interuniversity Institute of Bioinformatics in Brussels
• VIB: Vlaams Instituut voor Biotechnologie
• UGent: Universiteit Gent
• VUB: Vrije Universiteit Brussel
• Elixir BE: Elixir Belgium

Made in Belgium 🇧🇪

Footnotes

1. Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context, Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, and Lennart Martens Journal of Proteome Research 2020 19 (8), 3478-3486. DOI: 10.1021/acs.jproteome.0c00306. ↩