Docking with Methyl HMQC CSP data

HADDOCK
1

Hi there,

I am currently working on docking a ligand to a protein using CSP data obtained from HMQC Ile methyl NMR spectra. Since isoleucines are usually buried within the protein core, could you please advise me on how best to identify the active residues in this case?

In addition, I am using the web server for my calculations. Could you let me know how I might obtain “EXPERT” or “GURU” access in order to adjust the default parameters?

Many thanks for the help!

Best Regards,

Zhen

2

I am currently working on docking a ligand to a protein using CSP data obtained from HMQC Ile methyl NMR spectra. Since isoleucines are usually buried within the protein core, could you please advise me on how best to identify the active residues in this case?

You could in principle still use the ILE as active residues, but if they are not solvent accessible you might have to increase the distance for the restraints.
And on the server you will have to turn off the option to filter out buried residues.

Alternatively you could select the closest residue in the surface.

In addition, I am using the web server for my calculations. Could you let me know how I might obtain “EXPERT” or “GURU” access in order to adjust the default parameters?

Simply request it in your registration page.

3

Hi Alexdandre,

Thanks for your quick reply.
Are there any guidelines on how much I can increase the distance?

Best Regards,
Zhen