10.4 Evaluating Assemblies

Evaluating Assemblies (Module 10: The Assembler). Key concept: AF-Multimer validation and oligomeric state checks. Interpret AlphaFold-Multimer output: ipTM above 0.8 is confident, 0.6–0.8 is a grey zone, below 0.6 has likely failed.

• Interpret AlphaFold-Multimer output: ipTM above 0.8 is confident, 0.6–0.8 is a grey zone, below 0.6 has likely failed
• Read cross-chain PAE to judge whether the chains are placed relative to each other
• Test for unintended oligomeric states by running alternative stoichiometries
• Explain why ipTM is a confidence score and not a binding affinity or a free energy