Re: [modeller_usage] Evaluate protein-peptide complexes using modeller

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 03/20/2018 05:43 AM, SIMON KØNIG wrote:
> It has been pointed out to me that the evaluation method in modeller
> (molpdf, GA341 and DOPE) are not applicable for models of
> protein-peptide complexes.

There is an important difference here between scoring functions and 
assessment methods. molpdf is the scoring function used to guide the 
optimization of Modeller models - it is not designed for assessment and 
should not be used as such.

Many assessment functions are statistical in nature and so it's probably 
not a good idea to use them to assess a structure that wasn't 
represented in the training set. GA341 and DOPE were both trained on 
single chain globular proteins, so no, it's not a good idea to apply 
them to protein-peptide complexes. Check out SOAP at 
https://salilab.org/SOAP/ instead - there is a SOAP-Peptide potential 
that was specially trained for protein-peptide complexes.

	Ben Webb, Modeller Caretaker
--
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