Working with AlphaFold2, RoseTTAFold and other predicted models

You can use the predicted models from AlphaFold and other prediction software in Phenix. Using these models can be very helpful in structure determination because the models can be very accurate over much of their length and the models come with accuracy estimates that allow removal of poorly-predicted regions.

How to use predicted models in Phenix

Use Predict_and_build to incorporate predicted models in the structure solution workflow.

Predict_and_build generates predicted models and uses them to solve an X-ray structure by MR or to interpret a cryo-EM map. The tool then carries out iterative model rebuilding and prediction to improve the models. The iterative procedure allows creating more accurate predicted models than can be obtained with a simple prediction.

Predict and build can automatically generate a fairly accurate model starting from just a sequence file and either cryo-EM half-maps or X-ray data. Additionally, it provides morphed versions of unrefined predicted models that can be useful as reference models for refinement.

Use Predict_model to use the Phenix AlphaFold server to predict the structure of a protein chain.

Other tools for using predicted models: