Part 1. Critical use of AI for 3D structure prediction
Instructors: Benjamin Bardiaux (Permanent researcher in the Bacterial Transmembrane Systems Unit at Institut Pasteur) & Ludovic Sauguet (Research director in the Architecture & Dynamics of Biological Macromolecules Unit at Institut Pasteur)
Topics: What insights can an atomic model provide in a biological research project? How to critically analyze predicted 3D models? What can (will) you do with AI structure prediction?
Workshop overview: In the workshop you will acquire the theoretical and practical fundamentals for observing and manipulating 3D models of biological macromolecules. Through examples, you will learn how to predict structure(s) from sequence(s) and critically judge the quality of AI predicted 3D models. Examples of applications will range from the analysis of ligand and binding site to remote homology search and function annotation to understanding the role of quaternary structure.
Key words: AlphaFold, 3D structures/models, macromolecular complexes, ChimeraX.
Part 2. Make Your Own Protein from Scratch: Introduction to Protein Design
Instructors: Duc Duy Vu & Vincent Schnapka (Postdoctoral researchers at Institut Pasteur – CNRS), Computational Structural Biology Unit
Topics: How can you design a protein with a specific property, such as a protein binder? How can you improve the stability and solubility of the protein using design tools? What is the current state of the art in protein design? What are the limitations?
Workshop overview: In this workshop, you will gain both theoretical knowledge and practical skills in protein design. The session will begin with an introduction to the current state-of-the-art methods used in protein design. You will then explore a variety of showcase examples that illustrate different applications of protein design, including de novo protein design, protein binders, and strategies for enhancing stability and solubility.
Finally, you will have the opportunity to engage in hands-on practical exercises using relevant software tools. This will provide you with valuable experience and insights into the practical considerations necessary for successful protein design across various applications.
Key words: Protein design, de novo binder design, sequence redesign, motif-inpainting, AlphaFold hallucination, protein diffusion model. Prerequisites: intro to AI,basic usage of computer terminal and python
The workshop is open for all pasteurians. For more information and registration, please, visit this webpage.
