AlphaFold Protein Structure Prediction with ChimeraX

About this Class

Do you need to strengthen your structural biology skills? The NIAID Bioinformatics and Computational Biosciences Branch (BCBB) is offering training sessions over the next few weeks. Current topics include three series of practical training sessions on the following topics: 1) AlphaFold Protein Structure Prediction with ChimeraX The AlphaFold AI system has revolutionized protein structure prediction from sequence and has made obsolete most other methods. DeepMind, the creators of AlphaFold, have also collaborated with EMBL’s European Bioinformatics Institute to provide access to an online database of over 200 million predicted protein structures. UCSF ChimeraX is a free, multi-platform molecular modeling program which is actively integrating AlphaFold calculations and the AlphaFold database into its visualization platform. This workshop will comprise lecture and hands-on exercises that show how to get and evaluate AlphaFold prediction within ChimeraX. We will show how to download structures from the AlphaFold database. Students will learn how to submit AlphaFold calculations when pre-calculated structures are not available, and the situations when that may be necessary. We will also discuss how to use ChimeraX to interpret the two types of error predictions provided by AlphaFold calculations, as well as how UniProt integration into ChimeraX synergistically aids structure analysis.   Before attending the workshop, please download and install the ChimeraX Release Candidate 1.5 version of the program from the following website, and verify that it is working: https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.cgl.ucsf.edu%2Fchimerax%2Fdownload.html&data=05%7C01%7Cmaria.gomez%40nih.gov%7C350114eb9b1f4eab973d08dabb70f7ba%7C14b77578977342d58507251ca2dc2b06%7C0%7C0%7C638028391104184057%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=0Hy2%2B1l7JTmKIHHE%2BeaUcNNwG9CEgitfVQrdc1EkDaA%3D&reserved=0