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



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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             https://salilab.org/modeller/
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