carbonara - I2PC/scipion-courses GitHub Wiki

CARBonAra in Protein Design: Predicting sequence from carbon skeleton

  1. Step 1: Import human haemoglobin atom structure using the protocol import atomic structure appendix)

Import human haemoglobin atomic structure (step 1)

  1. Step 2: Extract chain A using the protocol chimerax operate appendix)

Extract chain A (step 2)

ChimeraX command lines:

1.- Select everything except the chain A of model #2:

  • sel ~ #2/A

2.- Remove it:

  • del sel

3.- Save the structure of chain A:

  • scipionwrite #2 prefix Hgb_chainA_

ChimeraX GUI chain A (step 2)

  1. Step 3: Sampling sequence for the chain A atomic skeleton with CARBonAra using the next protocol:

CARBonAra sampling sequence (step 3)

CARBonAra output

QUIZZ:

Which other residues could replace His 45, 58 and 87?

  1. Step 3: Sampling sequence for the chain A atomic skeleton with CARBonAra and sort the sequences by their AlphaFold scores : CARBonAra sampling sequence (step 3)