ADL: Autodock 4

Yang Ye leafyoung at yahoo.com
Fri Oct 19 03:16:39 PDT 2007


The analysis says that each result forms a cluster; there is no cluster 
found.

As I wrote before, docking a 20 peptide dock is a too ambitious move. 
The large negative energy shown is too bizaare for reasonable result. I 
doubt in the approach.

To retrieve structure from dlg file, I found Ad3's utility helpful. I 
attach get-docked script here.

Regards,
Yang Ye

On 10/19/2007 6:47 AM, IVYtony smth wrote:
> Hi Yang Ye,
>
> This is Tony Wang. I am the guy who posted a question regarding 
> docking a 20aa peptide onto a protein. I do find the "Histogram" in my 
> dlg file as follows. However, how do I interprete this diagram? and 
> How can I visualize the best docked conformation?
>
> Thanks a million!
>
> Tony
>
>     CLUSTERING HISTOGRAM
>     ____________________
>
> ________________________________________________________________________________
>      |           |     |           |     
> |                                   
> Clus | Lowest    | Run | Mean      | Num | 
> Histogram                         
> -ter | Binding   |     | Binding   | in  
> |                                   
> Rank | Energy    |     | Energy    | Clus|    5    10   15   20   25   
> 30   35
> _____|___________|_____|___________|_____|____:____|____:____|____:____|____:___
>    1 |-12423570391040.00 |   4 |-12423570391040.00 |   1 |#
>    2 |-11923820118016.00 |   1 |-11923820118016.00 |   1 |#
>    3 |- 11670521905152.00 |   9 |-11670521905152.00 |   1 |#
>    4 |-11182784118784.00 |   5 |-11182784118784.00 |   1 |#
>    5 |-11123252264960.00 |   8 |-11123252264960.00 |   1 |#
>    6 |-9930319855616.00 |  10 |-9930319855616.00 |   1 |#
>    7 |-9547153408000.00 |   2 |-9547153408000.00 |   1 |#
>    8 |-8967887519744.00 |   7 |-8967887519744.00 |   1 |#
>    9 |-8629512568832.00 |   6 |-8629512568832.00 |   1 |#
>   10 |-3623251869696.00 |   3 |- 3623251869696.00 |   1 |#
> _____|___________|_____|___________|_____|______________________________________
>
> -- 
> Signature: Success is a journey that never ends. 
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