De novo design of proteins using Rosetta and Alphafold 2
Thursday 23.06.2022, from 9:00 to 17:00
Great Lecture Hall, National Institute of Chemistry, Hajdrihova 19, Ljubljana, Slovenia
Protein design is of great technological importance and can solve many biomedically relevant challenges. Examples include new therapeutic agents (COVID-19 inhibitors, COVID-19 vaccines, flu inhibitors), nanomaterials (cages, layers, fibers) and sensors.
Are you interested in protein structure and would like to know more about the magic of de novo design? Then you are the perfect candidate!
The workshop is set up as a “crash course” in protein design, highlighting what is possible with current technology. Participants will learn how to build a four-helix bundle protein from scratch (i.e. using only mathematics). At the end of the workshop, they will obtain a sequence for the protein that folds into the designed structure. The basics of Rosetta, parametric backbone design, design of loops and design of side chains will be introduced. Alphafold 2 and it’s uses will also be presented.
Additional information:
Target audience: The workshop is intended for undergraduate and graduate students as well as postdocs and young scientist interested in protein design. Participants should know the basics of protein structure (what is an alpha helix, what are backbone and sidechains). The basics of Python (how to import modules and execute commands) is also recommended.
Prerequisites: Participants need to bring their own laptop. Google Colab will be used as the computational environment so only a browser is needed. Participants will also need a Google account.
Program
9:00 AM - 9:45 AM
Lecture
Introduction to protein design, PyRosetta and RosettaXML
9:45 AM - 10:30 AM
Workshop
Basics of Rosetta (pose, scoring, visualization, loading a PDB)
10:30 AM - 11:00 AM
Coffe Break
11:00 AM - 11:30 AM
Lecture
Parametric design of backbones .Check out an interactive helix bundle demo.
11:30 AM - 12:30 AM
Workshop
Parametric backbone design (and sampling tutorial)
12:30 AM - 13:30 AM
Lunch
13:30 AM - 14:00 AM
Lecture
Reside selectors, layer design, pack rotamers and minimisation
14:00 AM - 15:00 AM
Workshop
Loop design, layer design
15:00 AM - 15:30 AM
Coffe Break
15:30 AM - 16:00 AM
Workshop
Pack Rotamers, fast design
16:00 AM - 16:30 AM
Workshop
Filtering with Alphafold (RMSD, pLDDT)
16:30 AM - 17:00 AM
Concluding remarks
Speaker
dr. Ajasja Ljubetič
The workshop will be led by dr. Ajasja Ljubetič, a Marie Skłodowska-Curie Fellow that has trained in the Baker lab (Seattle, USA), one of the most famous protein design labs in the world.
Organizers
Ajasja Ljubetič, Eva Rajh, Tadej Satler
For more information contact: ajasja.ljubetic@ki.si
