Hi All,
I have recently used Cluspro to dock two of my proteins. I received my docked file and best model score model was named as Model000.000 something. Now, I would like to use this complex to find out the protein interface. My protein 1 is dimer and have two chains A,B. Protein 2 is monomer has chain A only.I tried Haddock, Pymol interface and whiscky to predict the interface,but the problem is the chain recognition in the complex generated from Cluspro. System can only selct 1 chain at a time. If I select chain A/B it quickly find the interface of the dimer of my protein A. How to solve this issue?
If you are using
http://www.protein.osaka-u.ac.jp/rcsfp/supracryst/suzuki/jpxtal/Katsutani/en/interface.php
when you talk about Pymol interface, you should be able to specify
interfaceResidue your_protein, chain A+B, chain C
to get the interface between a two-chain complex and a third chain.
Assuming that the docking algorithm gives the docked protein a unique chain label C. If this is not the case, you better change the chain label before docking, e.g. by using the "alter" command in Pymol (https://pymolwiki.org/index.php?title=Alter&redirect=no)
Try PISA server (www.ebi.ac.uk/pdbe/pisa/) and Dimplot (www.msg.ucsf.edu/local/programs/ligplot/man8.html) for protein-protein interactions.
Hi,
You can use below links:
http://www.bioinf.org.uk/intpred/
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
Thanks Annemarie Honegger for suggesting alter command. it really solved my problem. Can you suggest me to count the number of bonds in contacting residues?
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