Run Haddock without defining any residues?

HADDOCK
1

Is it possible to run Haddock without specifying any residues?

I would like to see if it predicts the residues for interfaces for proteins…

Or do I have to use CPORT or something similar to predict residues to provide to haddock?

2

There is an ab-initio mode available based on center-of-mass restraints between molecules. It does require expert level access. You can turn it on in the distance restraints menu.

This is actually described in our online CASP-CAPRI tutorial. See:

Another example of small molecule binding site screen in provided in the following online tutorial:

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3

On a side note, CPORT continuously has the following 2 predictors failing:

PPISP, ProMate

with errors:
Error messages of the failed predictors

PPISP

Exception in thread PPISPPredictionInput=>InterfacePredictionResult:

substring not found

ProMate

Exception in thread ProMatePredictionInput=>InterfacePredictionResult:

4

These are external servers. Not in our hands. Did you try direct submission of your system to those server to see if you get a successful prediction?