Homology Modelling with cofactors

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    • July 9, 2015 at 3:24 pm #2372
      Anonymous

        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.

      • September 4, 2015 at 11:23 pm #11190
        Anonymous

          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/molfile_to_params.py –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 section of the xml script, add: “add_hetatm=1”

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

        • September 9, 2015 at 6:02 am #11195
          Anonymous

            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.

          • February 3, 2016 at 1:45 pm #11411
            Anonymous

              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

               

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