[TALK 13] Structure Prediction and Design using AlphaFold – Sami Chaaban

Structure Prediction and Design using AlphaFold Speaker: Sami Chaaban, MRC Laboratory of Molecular Biology, UK In this video, Sami explains why we might need to prediction protein structure using AlphaFold modelling software. He briefly describes how it works. He details the key outputs of the program and how they can be used to assess the reliability of the predicted structures. He illustrates this with examples from his own scientific research and other projects within the LMB for single proteins and complexes using AlphaFold Multimer. He highlights the benefit of using Chimera or PAEViewer to visualise the error data. He gives tips on running your own sequence in AlphaFold2 via a webserver or ColabFold within the LMB. Then he explains the new features of AlphaFold3 and how it differs from AlphaFold2. He explains how crosslinking mass spec data can be incorporated in the predictions with AlphaLINK. He highlights potential issues in predictions that users need to beware of. Lastly, Sami describes how the program BindCraft can be used to design a protein binder to a target ab initio. To learn more on how to interpret AlphaFold structures see the EMBL-EBI series of talks: https://www.ebi.ac.uk/training/online... The Illustrated AlphaFold by Elana Simon, Jake Silberg is here: https://elanapearl.github.io/blog/202... Machine Learning Methods for Protein Modeling and Design Rosetta Commons    / @rosettacommons   Discover more about Sami’s research in the Andrew Carter lab at the LMB here: https://www2.mrc-lmb.cam.ac.uk/groups... Read more about software developed at the LMB here: https://mrclmb.ac.uk/science/lmb-deve... You can find more videos from the LMB 2025/26 Solving Problems with Molecular Techniques series here:    • Molecular Techniques Training Seminars 202...   -- About the MRC Laboratory of Molecular Biology (LMB): The LMB is one of the world's leading research institutes. Discoveries and inventions developed at the LMB, for example DNA sequencing and methods to determine the structure of proteins, have revolutionised all areas of biology. Our scientists work to advance understanding of biological processes at the molecular level. This information will help us to understand the workings of complex systems, such as the immune system and the brain, and solve key problems in human health. More links: Official Site: https://mrclmb.ac.uk/ Facebook:   / mrc.lmb   Bluesky: https://bsky.app/profile/mrclmb.bsky.... Instagram:   / mrc_lmb   LinkedIn:   / mrc-laboratory-of-molecular-biology   Click here to subscribe to MRC Laboratory of Molecular Biology on YouTube: https://www.youtube.com/user/LMBCambr...