Cport issue on large protein

HADDOCK
1

Hi
I am trying to use cport for this 8eeb protein using either the PDB import or the pdb fixed by CHARMM-GUI server (some residues are missing).
I am getting this error for job 19729511 using PBD import (8eeb):
Failed predictors
ProMate, PIER, SPPIDER, PINUP

PINUP has got seg fault so the problem is the size I guess. The other servers no idea:

**ProMate**
Exception in thread ProMatePredictionInput=>InterfacePredictionResult:
'NoneType' object has no attribute 'rfind'
**PIER**
Exception in thread PIERPredictionInput=>InterfacePredictionResult:

**SPPIDER**

Exception in thread SPPIDERPredictionInput=>InterfacePredictionResult:

Any suggestion? Since the protein is large but it is a transmembrane protein, I could in principle restrict the analysis on a small region of if, i.e. the extracellular one. Is it possible?

2

Any suggestion? Since the protein is large but it is a transmembrane protein, I could in principle restrict the analysis on a small region of if, i.e. the extracellular one. Is it possible?

Possibly. But there are currently issues with CPORT, both security ones and also several of the servers it is accessing are no longer working.Because of that we have discontinued the current server.

We are currently working on an updated version querying modern servers. But it will take some time before that one is ready for use in server form.

The code is however available on GitHub already: https://github.com/haddocking/cport

3

Thanks Alexandre. I will have look to the github. The modern servers you are referring to are thone reported in the cport github?

4

Actually using the pdb from CHARMM-GUI worked (almost):

the following predictors finished successfully
cons-PPISP (Chen and Zhou, 2005)
PINUP (Liang et al., 2006)

**Failed predictors**
ProMate, PIER, SPPIDER

Fair enough.

One more question on WHISCY. I have run blastp to get a set of hits and then aligned them using either MUSCLE or MAFFT. The aligned fasta to WHISCY give the following error:

whiscy_setup [ERROR] HSSP file could not be generated
ERROR: Setup has failed

Example attached.
clustalo-R20230503-171249-0115-13653860-p2m.fasta.txt (6.5 KB)

5

Thanks Alexandre. I will have look to the github. The modern servers you are referring to are thone reported in the cport github?

Yes