# Antibody docking with flexibility

**URL:** <https://ask.bioexcel.eu/t/antibody-docking-with-flexibility/657>\
**Category:** HADDOCK\
**Created:** [December 4, 2017, 4:21pm UTC](https://ask.bioexcel.eu/t/antibody-docking-with-flexibility/657 "2017-12-04T16:21:54Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![bercig](https://avatars.discourse-cdn.com/v4/letter/b/c77e96/32.png) [@bercig](https://ask.bioexcel.eu/u/bercig)\
**Post date:** [December 4, 2017, 4:21pm UTC](https://ask.bioexcel.eu/t/antibody-docking-with-flexibility/657/1 "2017-12-04T16:21:54Z")

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Dear all,

I am using HADDOCK’s easy interface to dock a modelled antibody structure to its antigen structure. I am planning keep the CDR3 loop of the antibody heavy chain fully flexible in the docking procedure to obtain better results. Can you please kindly guide me how can I do it ? I read it on the run.cns but I am not clear about it.

On the expert interface, under semi-flexible segments section, I should choose the ‘full’ option, and then, I should put the number of the initial and the last residue of the loops. Is this correct ?

Best regards

Bogac

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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:** [December 4, 2017, 6:42pm UTC](https://ask.bioexcel.eu/t/antibody-docking-with-flexibility/657/2 "2017-12-04T18:42:35Z")

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Use the fully flexible segment menu to specify the segments/loops to treat as fully flexible. It takes per segment two residue numbers (start and end of the segment).