# Prediction of residues binding to the target protein

**URL:** <https://ask.bioexcel.eu/t/prediction-of-residues-binding-to-the-target-protein/2552>\
**Category:** HADDOCK\
**Created:** [November 16, 2020, 10:42pm UTC](https://ask.bioexcel.eu/t/prediction-of-residues-binding-to-the-target-protein/2552 "2020-11-16T22:42:02Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Jane](https://avatars.discourse-cdn.com/v4/letter/j/ecb155/32.png) [@Jane](https://ask.bioexcel.eu/u/Jane)\
**Post date:** [November 16, 2020, 10:42pm UTC](https://ask.bioexcel.eu/t/prediction-of-residues-binding-to-the-target-protein/2552/1 "2020-11-16T22:42:02Z")

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Hi,  
I am very new in the field of protein. My question may be funny to you.  
Recently through co-ip experiment, I pull down two proteins with gene names:CLPX CPT1A. Now I want to know the residues for them to bind each other. I use Swiss-Model finding their PDB templates. I then use the PDB ID to do the Haddock docking. My HADDOCK run has finished successfully. I got the results. But I don’t know how to interpret the results. I don’t see the residues I am looking for. I am stucked here.  
Could you please help me check if my above reasoning make sense or not? Any input is greatly appreciated.  
Best regards,  
Jane

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 17, 2020, 7:46am UTC](https://ask.bioexcel.eu/t/prediction-of-residues-binding-to-the-target-protein/2552/2 "2020-11-17T07:46:53Z")

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Dear Jane

Probably best to start following first some of our online tutorials.

Visit [bonvinlab.org/education](http://bonvinlab.org/education) and check in particular the haddock2.4 tutorials.

In you case you could also try to do some bioinformatics predictions of interfaces to see what you get.  
Plenty of software/servers to do that, including our own CPORT and WHISCY servers.

Further you could do a contact analysis of all your models to see if there are “hot spot” regions in your proteins.  
Something similar in described in the following small molecule docking tutorial:

[https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/)

And in particular:

[https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/#statistical-contact-analysis](https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/#statistical-contact-analysis)