I had an assignment to dock Clarithromycin with two 23s rRNA ( one wild and one mutant )… I used HADDOCK 2.4 for this propose, with all default values. After getting the results I got 3 cluster for mutant and one for wild type and some graphical representation.

My question are-

- Was my approach correct?
- Why I hadn’t get equal no of clusters for both.
- How do I interpret which is the best cluster? and there are 4 structure in each cluster, so I do I know which structure is best in a respective cluster?
- What is the correct way to interpret the graphical data’s?
- For wild type my Z score was 0, but in mutant I got there there cluster and three z scores 1.3, -0.2, -1.1? which should i take? cause my hypothesis was "there will be better binding with wild type than mutant ".

I had an assignment to dock Clarithromycin with two 23s rRNA ( one wild and one mutant )… I used HADDOCK 2.4 for this propose, with all default values. After getting the results I got 3 cluster for mutant and one for wild type and some graphical representation.

First question is what kind of data did you use to guide the docking?

- Why I hadn’t get equal no of clusters for both.

Depends on the docking results.

- How do I interpret which is the best cluster? and there are 4 structure in each cluster, so I do I know which structure is best in a respective cluster?

Based on the HADDOCK core and and the first model within one cluster is always the one with the best (lowest) HADDOCK score.

- What is the correct way to interpret the graphical data’s?
- For wild type my Z score was 0, but in mutant I got there there cluster and three z scores 1.3, -0.2, -1.1? which should i take? cause my hypothesis was "there will be better binding with wild type than mutant “.

The z-score is purely a statistical measure. By definition if there is only one cluster it is 0. If two clusters, it will be +1 and -1.

I.e. should not be used to select clusters. It only tells you how many standard deviations is a cluster from the average score of all clusters

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Thank you for your reply and time. I think I understand the ans of my 2,3,4 & 5 th question. but please tell me my approach was correct…

But how do you define the interface then?

Default settings do require the definition of active residues.

Or did you do ab-initio docking?

I selected 1st 200 nucleotide as active residue as that was the limit showed there…

I.e. no information… In that case better to use the ab-initio mode of HADDOCK with centre of mass restraints

You will also have to increase the sampling.

Needs guru access.

Check out haddock2.4 tutorials are bonvinlab.org/education

Thank you so much for your guidance. I will try Ab-initio then…

Thank you So much for this Guidance… I will try ab initio then…