1. AlphaFold3 vs. Chai-1

Live Workshop Session

🎥 Live workshop recording — AlphaFold3 Structure Prediction: what's new and why it matters

Hands-On Exercise

  1. Setup for the activity
    1. In order to make a prediction with the AlphaFold server, you’ll need a Google account to sign in.
    2. In order to make a prediction with Chai-Lab, you’ll need to create a free account.
  2. Make a monomer prediction for 1QYS with both AF3 and Chai-Lab.
    1. AlphaFold 3:
      1. Paste in the sequence for 1QYS: MGDIQVQVNIDDNGKNFDYTYTVTTESELQKVLNELMDYIKKQGAKRVRISITARTKKEAEKFAAILIKVFAELGYNDINVTFDGDTVTVEGQLEGGSLEHHHHHH
      2. Press the “continue and preview job” button.
      3. Press “confirm and submit job”.
    2. Chai-Lab:
      1. Paste in the same sequence for 1QYS.
      2. Click “Run Job” to submit the prediction.
    3. Analysis:
      • How do the predicted structures compare to the native?
      • How does the AF3 prediction compare to Chai-Lab?
      • How confident is each model about its prediction?
  3. Make a multimer prediction for 8AJY with both AF3 and Chai-Lab.
    1. AlphaFold 3:
      1. Paste in the sequence for 8AJY_1 (chain A): MLTDRGMTYDLDPKDGSSAATKPVLEVTKKVFDTAADAAGQTVTVEFKVSGAEGKYATTGYHIYWDERLEVVATKTGAYAKKGAALEDSSLAKAENNGNGVFVASGADDDFGADGVMWTVELKVPADAKAGDVYPIDVAYQWDPSKGDLFTDNKDSAQGKLMQAYFFTQGIKSSSNPSTDEYLVKANATYADGYIAIKAGEPE
      2. Click “add entity”, make sure the molecule type to “protein”, and paste in the sequence of 8AJY_2 (chain B): MGSSHHHHHHSSGLVPRGSHMASKPQYRLGDVDFNGIIDGRDATAVLTEYARISTGKPAEFVGNTALAADVNKDNMIDAADATHILTYYAISSTRDDITSDDYFALHQPLRG
      3. The native structure was originally solved in the presence of 3 Ca2+ ions. Click “add entity”, change the molecule type to “ion”, and select Ca2+ to add each.
      4. Press the “continue and preview job” button.
      5. Press “confirm and submit job”.
    2. Chai-Lab:
      1. Paste in the sequence for 8AJY_1 (chain A).
      2. Click “Add Chain” and paste in the sequence for 8AJY_2 (chain B).
      3. Click “Add Ligand” and select “Ca2+” from the ion options. Repeat to add all 3 Ca2+ ions.
      4. Click “Run Job” to submit the prediction.
    3. Analysis:
      • How do the predicted structures compare to the native?
      • How does the AF3 prediction compare to Chai-Lab?
      • How confident is each model about its prediction?
      • What about the placement of the ions and the coordinating side chains?
  4. Make a protein-ligand prediction with Chai-Lab for 2JIE (beta-glucosidase with 2-fluoro-glucose).
    1. Chai-Lab:
      1. Paste in the sequence for 2JIE (beta-glucosidase B): MHHHHHHSENTFIFPATFMWGTSTSSYQIEGGTDEGGRTPSIWDTFCQIPGKVIGGDCGDVACDHFHHFKEDVQLMKQLGFLHYRFSVAWPRIMPAAGIINEEGLLFYEHLLDEIELAGLIPMLTLYHWDLPQWIEDEGGWTQRETIQHFKTYASVIMDRFGERINWWNTINEPYCASILGYGTGEHAPGHENWREAFTAAHHILMCHGIASNLHKEKGLTGKIGITLNMEHVDAASERPEDVAAAIRRDGFINRWFAEPLFNGKYPEDMVEWYGTYLNGLDFVQPGDMELIQQPGDFLGINYYTRSIIRSTNDASLLQVEQVHMEEPVTDMGWEIHPESFYKLLTRIEKDFSKGLPILITENGAAMRDELVNGQIEDTGRHGYIEEHLKACHRFIEEGGQLKGYFVWSFLDNFEWAWGYSKRFGIVHINYETQERTPKQSALWFKQMMAKNGF
      2. Click “Add Ligand” and select “Custom SMILES”.
      3. Enter the SMILES string for 2-fluoro-glucose (G2F): OCC1OC(O)C(F)C(O)C1O
      4. Click “Run Job” to submit the prediction.
    2. Analysis:
      • How does the predicted structure compare to the crystal structure (2JIE)?
      • Is the ligand positioned correctly in the active site?
      • How well does Chai-Lab predict the protein-ligand interactions?
      • What is the confidence score for the ligand placement?