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