# Small ligand binding site screening

**URL:** <https://ask.bioexcel.eu/t/small-ligand-binding-site-screening/642>\
**Category:** HADDOCK\
**Created:** [November 27, 2017, 9:15am UTC](https://ask.bioexcel.eu/t/small-ligand-binding-site-screening/642 "2017-11-27T09:15:43Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\
**Post date:** [November 27, 2017, 9:15am UTC](https://ask.bioexcel.eu/t/small-ligand-binding-site-screening/642/1 "2017-11-27T09:15:43Z")

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I would like to carry out ab-initio binding site screening for my ligand Taxol. However, i would like to know is it applicable since my supervisor say it is only for small ligand. Any how do we know if a molecule can be categorize as small molecule in this case? Would appreciate if anyone can explain.

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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 27, 2017, 6:22pm UTC](https://ask.bioexcel.eu/t/small-ligand-binding-site-screening/642/2 "2017-11-27T18:22:48Z")

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You can try… But there is simply no warranty on the results… Taxol is a challenging case.  
Try first reconstituting a known complex and see what you get.

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**Author:** ![shawnteh1711](https://avatars.discourse-cdn.com/v4/letter/s/3da27b/32.png) [@shawnteh1711](https://ask.bioexcel.eu/u/shawnteh1711)\
**Post date:** [November 28, 2017, 12:46am UTC](https://ask.bioexcel.eu/t/small-ligand-binding-site-screening/642/3 "2017-11-28T00:46:00Z")

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I try both vinblastin and taxol using 1z2b and 1jff without ab-initio. I am using all interacting residue (hydrogen bond and non-hydrogen bond stated in PDBsum) as active residue, passive resiude define automatically. However, both docked result seem close but not expectantly same with reference ligand crystal using ligplot. Some of the interaction is not the same with PDBSUM.

![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/46612325729eb0317d2b8b446a78dfb134f26152.png)

![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/761c2960bedee865f4549d97af66d02c1bfab24a.png)

![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/2c0787c2884a5e57ed226da167faf7ce939fc50e.jpg)  
ligand taxol not bind into binding site

![image](https://dub1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/89174087dca6fbe4d6c30ebc8000944558df3bef.jpg)  
original taxol bind directly into binding site

Would appreciate if anyone can explain how to improve the docking ?