bio2byte/scop3p-toolkit repository overview

⁠About Scop3P

Scop3P provides a unique and powerful resource to explore and understand the impact of phospho-sites on human protein structure and function, and can thus serve as a springboard for researchers seeking to analyse and interpret a given phosphosite or phosphoprotein in a structural, biophysical, and biological context. The resource re-uses public domain data from a variety of leading international resources, including UniProtKB and PDB, but also uses reprocessed mass spectrometry-based phospho-proteomics data from PRIDE/ProteomExchange, which is in turn globally collected and thus wholly international-driven.

Scop3P is developed at Ghent University and is online since June 2019. The publication describing Scop3P is available here.

⁠The Scop3P Toolkit

Protein phosphorylation context across sequence, structure, proteomics, and variant evidence.

⁠Quick start

Start the container:

docker run --rm -it -p 8000:8000 bio2byte/scop3p-toolkit:0.1.0

Then, open http://localhost:8000⁠ using your web browser.

⁠Applications/Module

The Scop3P toolkit is a set of tools for exploring and extending Scop3P features written as a Shiny App in Python.

⁠Peptide Mapper

• Loads peptide and modification data from Scop3P
• Filters and selects peptide spans
• Maps selections on AlphaFold structures
• Exports a styled HTML session

⁠Structure Visualisation

• Fetches PTMs and disease-associated variants
• Renders PDB or AlphaFold structures
• Runs Bio2Byte predictions and 3D coloring
• Builds residue interaction networks
• Runs TM-align comparisons

⁠Mutation Effect

• Fetches WT UniProt sequence and Scop3P PTMs
• Runs Bio2Byte WT and mutant predictions
• Compares WT vs mutant residue features
• Generates mutation-centric inference summaries

⁠About

Scop3P is part of the ELIXIR Belgium infrastructure as a Core Service since 2020: Learn more⁠.

• You can find data and documentation (in PDF) here⁠.
• Official documentation of the Scop3P REST API: Swagger OpenAPI definition⁠.

⁠Contact us

Scop3P Toolkit has been developed in Belgium by CompOmics (UGENT) in collaboration with the Bio2Byte Lab (VUB) and the VIB Data Core team (VIB):

For any further questions, feedback or suggestions, please send an email to: [email protected]⁠, or [email protected]⁠.