BioExcel Webinar #7: PRODIGY, a web server to predict binding affinities in protein-protein complexes


#1

This topic is for all discussions related to the webinar, “Integrative Structural Biology and Modelling” which took place on Wednesday 12th October.

If you have any questions in response to the webinar, please post them here, and we’ll do our best to answer them (whether it’s immediately after the live webinar, or if you have arrived here from YouTube).


#2

Click here to watch the webinar: Webinar 7: PRODIGY


#3

Question from the talk: Why was 5.5 Å used as the contact cut-off?


#4

Presenter’s answer: It has been optimised. We tried vales between 3 Å and 20 Å and we picked the value with the best correlation.


#5

Question from the talk: Is there a size limitation between Interactor 1 and Interactor 2? Did you perform any correlation between size of interactions and binding prediction?


#6

Presenter’s answer: We didn’t see any particular correlation between the size of the interaction itself, although the benchmark we used also has big cases. The biggest was – more or less – the one resulting from antibodies. Very big cases might have an impact but we didn’t see anything relevant from the benchmarks we used.


#7

Hi. Is PRODIGY supported protein-RNA and protein-DNA complexes (because of comparing binding affinity)?


#8

PRODIGY has only been parametrised so far for protein-protein complexes.
This might change in the future.


PRODIGY-Hi. Is PRODIGY supported protein-RNA and protein-DNA complexes (because of comparing binding affinity)?
#9

many thanks. and what’s your suggestion?