Protein complex structure prediction with AlphaFold and protein structure visualization with ChimeraX
Course Details:
Date: 26 November 2024 (Tuesday)
Time: 13:00-17:30
Location: IMB Seminar Room
Course Instructors: Dr Katja Luck & Dr Jesús Alvarado Valverde
Target group: PhD students & postdocs
Seats available: 30 participants on-site (possible online)
Course Description:
AlphaFold represents a breakthrough in molecular biology research for the generation of structural models of protein complexes. However, AlphaFold almost always returns a structural model. Assessing if the model is likely accurate or inaccurate is rarely trivial. Furthermore, AlphaFold often cannot produce an accurate structural model for two interacting proteins, if long protein fragments or full length sequences are submitted for structure prediction.
This course will teach participants how to design submissions to AlphaFold that are more likely to result in a confident structural model of a protein complex, how to assess if the model is likely accurate, and how to visualize protein structures with ChimeraX for the sake of model assessment and figure generation. During the course, participants will learn how to submit multiple jobs at once to the local AlphaFold-Multimer v2 installation at IMB via the novel user interface Fold2Go and how to retrieve results. The course will also discuss on the pros and cons about using AlphaFold v2 or v3.
Course Preparation:
As a pre-requisite for this course, participants should know the structure of the 20 amino acids and their properties as well as which amino acids can form hydrophobic contacts, H-bonds or salt bridges. The course consists of both theoretical and hands-on practical exercises. As such, participants will need to bring along their own laptops to join in the practical exercises. Additionally, participants can use a protein pair of interest for the practical exercise.
Further information on preparation of the course will be communicated directly to selected participants once registration closes.
Interested? Register now via this link. Deadline for registration is 27 October 2024.