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Assess protein dynamics & post-translational modifications through ELIXIR Belgium Node services: B2BTools & Scop3P

Lesson overview

Description
The breakthrough of AlphaFold2 delivered structural models for nearly all proteins lacking experimental structures, opening new avenues to interrogate both sequence and structure. However, these models capture static snapshots rather than the dynamic conformational ensembles that govern protein behaviour.

The Bio2Byte Tools, published as B2BTools, is a suite of sequence-based predictors for unveiling the biophysical properties hidden in the amino acid language with ease: backbone dynamics, early folding events, disordered positions among other features. Developed by the lab led by Prof. Dr. Wim Vranken, this online platform is part of the ELIXIR Belgium node services. In parallel to this suite of tools, Scop3P, another ELIXIR Belgium node service, will allow you to explore and understand the impact of phospho-sites on human protein structure and function. It can serve as a springboard for researchers seeking to analyse and interpret a given phosphorylation site or phosphoprotein in a structural, biophysical, and biological context.

Prerequisites
Basic knowledge on proteins, protein structures are a plus. Python language skills are recommended (not mandatory) to follow the Jupyter Notebook examples on Google Colab platform.

Learning Outcomes:
By the end of the course, learners will be able to:

  1. Calculate and analyse protein biophysical profiles for sequence-based data.
  2. Perform exploratory structural analysis combining the AlphaFold predictions with biophysical profiles generated by the B2BTools.
  3. Compare the impact on protein dynamics by introducing mutations with B2BTools.
  4. Able to correlate biophysical properties to post-translational modifications (PTMs).

Target Audience: All scientists and technical staff, all interested in working with protein dynamics, all researchers and industry professionals.

Level: Beginners.

License: Creative Commons Attribution 4.0 International License

Funding: This project has received funding from VIB.

Authors

Pathmanaban Ramasamy

Pathmanaban Ramasamy


CompOmics/UGent, ELIXIR-BE

Adrián Díaz

Adrián Díaz


Bio2Byte/VUB, ELIXIR-BE

Citing this lesson

Please cite as:

  1. Pathmanaban Ramasamy, Adrián Díaz (2026). Training Material: Assess protein dynamics & post-translational modifications. Zenodo. https://doi.org/10.5281/zenodo.18242776.
  2. Jose Gavalda-Garcia, Adrián Díaz, Wim Vranken. (2024). bio2Byte Tools deployment as a Python package and Galaxy tool to predict protein biophysical properties. Bioinformatics, Volume 40, Issue 9, September 2024, btae543. doi.org/10.1093/bioinformatics/btae543 1.
  3. Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, Wim Vranken, b2bTools: online predictions for protein biophysical features and their conservation, Nucleic Acids Research, Volume 49, Issue W1, 2 July 2021, Pages W52–W59. doi.org/10.1093/nar/gkab425 2.
  4. Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, & Lennart Martens. (2020). Scop3P: A Comprehensive Resource of Human Phosphosites within Their Full Context. Journal of Proteome Research 2020 19 (8), 3478-3486. 10.1021/acs.jproteome.0c00306 3.

Training Template

Please cite as:

  1. Geert van Geest, Elin Kronander, Jose Alejandro Romero Herrera, Nadja Žlender, & Alexia Cardona. (2023). The ELIXIR Training Lesson Template - Developing Training Together (v1.0.0-alpha). Zenodo. doi.org/10.5281/zenodo.7913092 4.

Setup

To run this course you need to:

  • Have in mind a TOKEN that will be used to access your B2BTools predictions.
  • A Google Account (in general, your @gmail.com email) to login on Google Colab.

  1. Jose Gavalda-Garcia, Adrián Díaz, and Wim Vranken. Bio2byte tools deployment as a python package and galaxy tool to predict protein biophysical properties. Bioinformatics (Oxford, England), 40(9):btae543, September 2024. URL: https://europepmc.org/articles/PMC11873786, doi:10.1093/bioinformatics/btae543. ↩

  2. Luciano Porto Kagami, Gabriele Orlando, Daniele Raimondi, Francois Ancien, Bhawna Dixit, Jose Gavaldá-García, Pathmanaban Ramasamy, Joel Roca-Martínez, Konstantina Tzavella, and Wim Vranken. B2btools: online predictions for protein biophysical features and their conservation. Nucleic Acids Research, 49(W1):W52–W59, 05 2021. URL: https://doi.org/10.1093/nar/gkab425, arXiv:https://academic.oup.com/nar/article-pdf/49/W1/W52/38842326/gkab425.pdf, doi:10.1093/nar/gkab425. ↩

  3. Pathmanaban Ramasamy, Demet Turan, Natalia Tichshenko, Niels Hulstaert, Elien Vandermarliere, Wim Vranken, and Lennart Martens. Scop3p: a comprehensive resource of human phosphosites within their full context. Journal of proteome research, 19(8):3478—3486, August 2020. URL: https://doi.org/10.1021/acs.jproteome.0c00306, doi:10.1021/acs.jproteome.0c00306. ↩

  4. Geert van Geest, Elin Kronander, Jose Alejandro Romero Herrera, Nadja Žlender, ELIXIR Training Coordination Team, and Alexia Cardona. The elixir training lesson template - developing training together. May 2023. URL: https://doi.org/10.5281/zenodo.7913092, doi:10.5281/zenodo.7913092. ↩