How to generate ambig.tbl for blind docking

[zhouzheng2000zzbera]

Dear HADDOCK3 Development Team,

I hope this message finds you well. I am currently looking to perform batch docking between various proteins and peptides to identify candidate proteins. However, I am working with completely unknown proteins. Could you please guide me on how to generate the ambiguous interface constraints (ambig.tbl) for blind docking?

I would greatly appreciate your assistance.

Thank you very much for your time and help!

Best regards,

[VGPReys]

Hi there,

Thanks for your interest in using haddock3 for your research !

Basically three options can do ab-initio docking.

• Center of mass restraints: for this, turn cmrest = true in [rigidbody] and [flexref] modules and contactairs = true in subsequent CNS modules.
• Random airs: for this, turn ranair = true in [rigidbody] and contactairs = true in subsequent CNS modules.
• Surface restraints: for this, turn surfrest = true in [rigidbody], either contactairs = true or cmrest = true in [flexref] and contactairs = true subsequent CNS modules.

We have been performing small benchmarks (on HADDOCK2.5) on what is the best ab-initio solution, and it seems that the 2nd option was giving slight better results, but not significant.

Do not forget to increase the sampling in [rigidbody] as the it basically relies on trials and errors to find a good solution.

Hope this helps,

Cheers

[zhouzheng2000zzbera]

Hi there,

Thank you so much for the detailed and helpful response! I really appreciate the guidance on the different options for ab-initio docking. I'll make sure to increase the sampling in [rigidbody] as you suggested.

Thanks again for your support!

Cheers