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Homology Modelling with cofactors

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Homology Modelling with cofactors

Hi guys,

Can the RosettaCM protocol include cofactors as residues/restraints in model building?

I am building a cytochrome P450 model and I'd like to include the haem if possible. Without the haem, some of the cofactor-interacting backbone has subtle conformational differences.

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Thu, 2015-07-09 08:24
Derek Smith

Here's what Frank Dimaio recommends for doing cofactors with RosettaCM:

1) generate params and cartesian restraints using Ian's script:
python ~/rosetta_source/src/python/apps/public/ --keep-names --clobber --extra_torsion_output --centroid LIG.mol2 -p LIG -n LIG
2) give the extra params file to Rosetta:
--extra_res_cen LIG.cen.params
--extra_res_fa LIG.fa.params
--extra_improper_file LIG.tors
3) add the ligand(s) in all the template files(*), numbering them sequentially after the chainlength (so if the input fasta has 100 aas, ligands would start at 101).
4) in the <Hybridize ... /> section of the xml script, add: "add_hetatm=1"

(*) I presume this would be the *post threading* template files.

Fri, 2015-09-04 16:23

Thanks Rocco!

I will give this a try.

I have one more question about RosettaCM, but I will add that to the 'Multiple Templates' thread.

Tue, 2015-09-08 23:02
Derek Smith

Hi Rocco,

Just to confirm this works *really* well!

Based on your (and Frank's) recommendations, I recently incorporated S-adenosylmethionine into a model enzyme using RosettaCM. A couple of pointers for anyone else wanting to do this:

- Make sure all threaded parent template files have the ligand coordinates

- Make sure 'HETATM' is replaced with 'ATOM' in the template files

- No need to add a chain break at the end of the sequence file


Wed, 2016-02-03 05:45
Derek Smith