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selecting Hetatoms for simultaneously docking
https://www.dockingserver.com/forum/viewtopic.php?f=2&t=14
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Author:  zelepuga [ Sat May 30, 2009 10:44 am ]
Post subject:  selecting Hetatoms for simultaneously docking

The enzyme has a co-factor. I want to dock the substrate to the same cavity with the co-factor simultaneously. How should I Select simulation box ( and select Hetatoms!) to prepare the protein for docking? Any help will be appreciated. Thanks.

Author:  bikadi [ Tue Jun 02, 2009 7:43 pm ]
Post subject:  Re: selecting Hetatoms for simultaneously docking

Simply select the co-factor in the protein clean page in the select hetatoms box (if the cofactor is heme, it is automatically selected), then it will be involved in docking.

Author:  lucska [ Wed Oct 09, 2013 2:37 pm ]
Post subject:  Re: selecting Hetatoms for simultaneously docking

Hello, I have the same problem. I need a cofactor for my docking. So I tried to choose it in heteroatom box in clean protein page...late I use this protein for docking but I didn't see my cofactor in docking results (section reference ligands contains only ligand that should be deleted, no cofactor). Please can you give me an advise? Thank you

Author:  bikadi [ Wed Oct 09, 2013 6:50 pm ]
Post subject:  Re: selecting Hetatoms for simultaneously docking

Could you please send me a link to your calculation? It is possible that the cofactor is there just you cannot see it so I should check this first.

Thanks,
Zsolt

Author:  lucska [ Tue Oct 15, 2013 12:22 pm ]
Post subject:  Re: selecting Hetatoms for simultaneously docking

bikadi wrote:
Could you please send me a link to your calculation? It is possible that the cofactor is there just you cannot see it so I should check this first.

Thanks,
Zsolt


Thank you for your quick response. I try it again and better:-) But I still don't see the cofactor...Here is the link to my calculation (http://www.dockingserver.com/web/docking/210949/). I registered, so I don't know if you can see it. I'm really beginer, so i don't know if my results are ok. Thank you.

Author:  bikadi [ Wed Oct 16, 2013 6:26 pm ]
Post subject:  Re: selecting Hetatoms for simultaneously docking

Hi,

the NAPD is there in the docked structure but it is very far away from the simulation box you used for docking.

Best Regards,
Zsolt

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