Re: [modeller_usage] some food for thought...

[Cvetan Stojkoski <>]

Yes, you can use a template containing more than one chain for modelling.

Use a modeller script to extract the protein sequence from the pdb file 
containing both chains and use that for your alignment.

READ_MODEL FILE = 'pdb_file_name' #Without the extension
SEQUENCE_TO_ALI ALIGN_CODES = 'pdb_file_name', ATOM_FILES = ALIGN_CODES
WRITE_ALIGNMENT FILE = 'pdb_file_name.seq'

The above script should do that for you. You can also produce a model of a 
complex provided you have a template containing the two proteins.

Cvetan

Quoting Himanshu Grover <>:

> Hullo,
>     am a novice user of modeller... need some help for a problem described
> below...
> 
> my target protein contains 2 chains which need to be modelled. I am
> currently modelling them independently and then concatenating their pdbs
> to get the complete protein.
> 
> Firstly, is is possible to model the 2 chains together, rather than
> independently, since that would mean taking one chain into context while
> modelling the other...
> 
> Secondly, after generating the protein, i need to check its binding to
> another protein, with which it is always found complexed. For instance, in
> case of immunoglobulins, we have 2 chains to be modelled, and then these
> chains are always found complexed with a peptide-MHC... So I need that the
> optimization of the chains and loop refinement of the heavy and the light
> chains should take place taking into consideration the peptide-MHC as
> well.
> 
> The reason i want to do this is that I tried to generate the structure of
> some xyz protein through modeller, whose crystallographic structure is
> also available. so i took xyz(crystallographic) as the template and tried
> to generate the same structure with modeller. the new struc. has an rmsd
> value of 0.19 as compared to the actual structure, which is quite good.
> however, at the binding site, there are some side chains that are not
> nicely fitting on top of the actual structure. and some interactions have
> gone down, resulting in poor binding. is there a way to rectify this
> problem?? i was thinking of doing the simulated annealing part taking into
> context the entire complex... that is, say, after we
> concatenate the light and heavy chain of immunoglobulin with p-MHC, and
> then applying molecular dynamics taking into consideration p-MHC
> also...but am not sure whether that is possible or not... any say??
> 
> sincerely,
> himan...
> 
> 
> 
> _______________________________________________
> modeller_usage mailing list
> 
> http://salilab.org/mailman/listinfo/modeller_usage
>