From_sequence_to_model - I2PC/scipion-courses GitHub Wiki

1.- Get the initial model looking for homologous proteins

Basics in homology modeling: We need look for a template to provide the structure to borrow and build a MSA to stablish the best sequence correlation between template and target.

Modeling workflow to get the first model of the alpha subunit of the human haemoglobin using a sequence homologous template (upper part of the alpha subunit modeling workflow):

From sequence to model section

Auxiliary information

Specimen PDB UniProt EMDB
HEMOBLOGIN 1PBX P69905 3488
  1. Step 1b: Import human haemoglobin alpha subunit sequence (details in modeling tutorial and protocol appendix)

Import human haemoglobin alpha subunit sequence (step 1.b)

  1. Step 5a: Import atomic structure to be used as model template (details in modeling tutorial and protocol appendix)

Import atomic structure (step 5.a)

  1. Steps 5b, 5c, 5d and 5e: Import additional sequences to prepare your sequence alignment (details in modeling tutorial and protocol appendix)

Import additional sequences (steps 5.b, 5.c, 5.d and 5.e)

  1. Step 6a: ChimeraX model_from_template protocol to get the first approximation to the atomic structure of the human Hgb alpha subunit (details in modeling tutorial and protocol appendix)

Model_from_template protocol (step 6.a)

Once ChimeraX GUI is opened:

Go to Tools -> Sequence -> Modeller Comparative

  1. Modeller menu to retrieve human Hgb alpha subunit models based on sequence homology (details in modeling tutorial and protocol appendix)

Modeller menu (step 6.a)

At this point wait for a while until the retrieved models appear.

Once you have the retrieved models, select one of them, for instance #3.2. Complete the model with the HEME group from the atomic structure used as template, and save it in Scipion with the next command lines:

1.- Rename model #3.2 as #4.

  • rename #3.2 id #4

2.- Save chain A of the renamed model in tmp folder.

  • save /tmp/chainA.cif format mmcif models #4

3.- Open saved chain A as model #4; hide the rest of the models and observe that HEME group is still missing.

  • open /tmp/chainA.cif

4.- Borrow HEME group from template model #2. First select it.

  • select #2/A:144

5.- Then save it in tmp folder.

  • save /tmp/HEME.cif format mmcif models #2 selectedOnly true

5.- Open HEME group as model #5.

  • open /tmp/HEME.cif

6.- Combine chain A and its respective HEME group (models #4 and #5 to generate model #6).

  • scipioncombine #4,5

7.- Save this new model #6 as the alpha subunit of the human Haemoglobin.

  • scipionwrite #6 prefix Hgb_alpha_

ALTERNATIVE TO COMMANDS 1-8:

  • rename #3.2 id #4

  • select #4

  • select add #2/A:144

  • delete ~ sel

  • scipioncombine #2,4 modelid 10

  • scipionwrite #10 prefix Hgb_alpha_

QUIZZ: Is the result identical to the previous one? Answer this question after running the next step of the workflow (6c).

  1. Step 6c: Recovering of previous ChimeraX session (details in modeling tutorial and protocol appendix)

Recover session (step 6.c)