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 -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage