mol_model_course_2023

Workshop: Protein structure modelling in Modeller

Description

Jupyter notebook

AlphaFold2

Required software and resources

Learning resources

Assignments

Modeller (based on tutorial)

  1. Build model for lactate dehydrogenase from Trichomonas vaginalis (TvLDH) based on a single template. Perfom loop refine by LoopModel, DopeLoopModel.
  2. Compare plots of energy score (DOPE) for model, template, model with auto loop refine, model with Dope loop refine.

AlphaFold2

  1. Predict 3D structure of your protein (choose small one or fragment); use one of ChimeraX or Collab. Add sequence coverage plot and structure image.

Troubleshooting