# DNA ligand Complex

**URL:** <https://ask.bioexcel.eu/t/dna-ligand-complex/1802>\
**Category:** PRODIGY\
**Created:** [January 22, 2020, 6:46am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802 "2020-01-22T06:46:41Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![attaribinm](https://avatars.discourse-cdn.com/v4/letter/a/87869e/32.png) [@attaribinm](https://ask.bioexcel.eu/u/attaribinm)\
**Post date:** [January 22, 2020, 6:46am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/1 "2020-01-22T06:46:41Z")

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Hi  
I want to calculate the binding affinity of dsDNA ligand complex. Which interface of prodigy web server should i use i.e prodigy, prodigy protein ligand or prodigy crystal?

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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:** [January 22, 2020, 7:08am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/2 "2020-01-22T07:08:49Z")

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None of those support DNA. We don’t have any software for this.

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<div class="post-metadata">

**Author:** ![attaribinm](https://avatars.discourse-cdn.com/v4/letter/a/87869e/32.png) [@attaribinm](https://ask.bioexcel.eu/u/attaribinm)\
**Post date:** [January 22, 2020, 7:17am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/3 "2020-01-22T07:17:36Z")

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@amjjbonvin mjjbovin Sir i got the results about above mentioned complexes by using prodigy protein ligand interface. That means these are not reliable?

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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:** [January 22, 2020, 7:29am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/4 "2020-01-22T07:29:27Z")

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Was never tested / benchmarked for protein-DNA…

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<div class="post-metadata">

**Author:** ![attaribinm](https://avatars.discourse-cdn.com/v4/letter/a/87869e/32.png) [@attaribinm](https://ask.bioexcel.eu/u/attaribinm)\
**Post date:** [January 22, 2020, 7:38am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/5 "2020-01-22T07:38:13Z")

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Sir  
In output folder even i got IC\_List file containing information about contact residues along with stat folder. So, can we use this as a logic that prodigy protein ligand interface can be used for DNA ligand complex too?

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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:** [January 22, 2020, 7:52am UTC](https://ask.bioexcel.eu/t/dna-ligand-complex/1802/6 "2020-01-22T07:52:11Z")

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It is giving contacts, but has never been tested for protein-DNA complexes.  
No idea what the accuracy is. Use it at your own risk.