# Docking of Clarithromycin which is a macrolide, with 23s r-RNA **URL:** \ **Category:** HADDOCK\ **Created:** [September 29, 2022, 11:20am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918 "2022-09-29T11:20:16Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 29, 2022, 11:20am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/1 "2022-09-29T11:20:17Z")
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- 1. Was my approach correct? 2. Why I hadn’t get equal no of clusters for both. 3. 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? 4. What is the correct way to interpret the graphical data’s? 5. 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 ". ---
**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:** [September 29, 2022, 11:47am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/2 "2022-09-29T11:47:55Z")
> 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? > 1. Why I hadn’t get equal no of clusters for both. Depends on the docking results. > 1. 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. > 1. What is the correct way to interpret the graphical data’s? > 2. 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 ---
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 29, 2022, 12:30pm UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/3 "2022-09-29T12:30:09Z")
1. For your 1st question I build 3d structure of rRNA using 3DRNA web server and i used pdb file of Clarithromycin. Then i perform entirely on default settings. ---
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 29, 2022, 12:33pm UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/4 "2022-09-29T12:33:08Z")
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… ---
**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:** [September 30, 2022, 11:24am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/5 "2022-09-30T11:24:25Z")
But how do you define the interface then? Default settings do require the definition of active residues. Or did you do ab-initio docking? ---
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 30, 2022, 11:42am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/6 "2022-09-30T11:42:21Z")
I selected 1st 200 nucleotide as active residue as that was the limit showed there… ---
**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:** [September 30, 2022, 11:58am UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/7 "2022-09-30T11:58:48Z")
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](http://bonvinlab.org/education) ---
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 30, 2022, 12:00pm UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/8 "2022-09-30T12:00:45Z")
Thank you so much for your guidance. I will try Ab-initio then… ---
**Author:** ![Pratanuk](https://avatars.discourse-cdn.com/v4/letter/p/a88e4f/32.png) [@Pratanuk](https://ask.bioexcel.eu/u/Pratanuk)\ **Post date:** [September 30, 2022, 12:01pm UTC](https://ask.bioexcel.eu/t/docking-of-clarithromycin-which-is-a-macrolide-with-23s-r-rna/3918/9 "2022-09-30T12:01:29Z")
Thank you So much for this Guidance… I will try ab initio then…