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Protein Structure Prediction

Explore computational methods for protein structure prediction including homology modeling, AlphaFold, and molecular dynamics simulations for understanding protein function.

Protein Structure Prediction

Syllabus

Foundations3 lessons
  1. Levels of protein structure: primary to quaternary10 min
  2. Why structure matters and the folding problem11 min
  3. Experimental structures: X-ray, NMR and cryo-EM12 min
Template-based modeling3 lessons
  1. Homology modeling: principles and the pipeline11 min
  2. Building a model with SWISS-MODEL and MODELLER12 min
  3. Threading and fold recognition12 min
The deep-learning era4 lessons
  1. The AlphaFold2 revolution11 min
  2. How AlphaFold thinks: MSA, coevolution and the Evoformer12 min
  3. Running predictions with ColabFold12 min
  4. Reading confidence: pLDDT and PAE12 min
Validation and downstream4 lessons
  1. Assessing model quality: Ramachandran, clashes and MolProbity11 min
  2. Limitations: disorder, multimers and conformational change11 min
  3. Putting predicted structures to work12 min
  4. Wrap-up: a prediction workflow and where to go next11 min