ADL: Thanks for your Autodock help

Bagdevi bagdevi.mishra at gmail.com
Tue Jun 2 11:39:01 PDT 2009


In case of castP, I feel, the unit of the area and volume is in
angstrom. They have not mentioned it anywhere, Thus for confirmation,
you can better contact the people who made it.

"Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron
Turpaz, and Jie Liang. 2006. CASTp: computed atas of surface
topography of proteins with structural and topographical mapping of
functionally annotated residues. Nucl. Acids Res., 34:W116-W118."

And when you say, showing the pocket with space-filled, if you mean,
you want the space of the cavity and not the residues making it, this
can be done using PASS software. This software gives the cavities as
filled beads, and does not give any information about which residues
or atoms make this cavity. when you give a pdb file as input, it gives
u two files as output, 1. <file>.probes.pdb - this have all the
cavities of the protein space filled and 2. <file>.asps.pdb - this
file will have the coordinate of the centre of the each cavity
mentioned in the probes.pdb file. you can view these two files with
any standard molecule viewer along with the input file to understand
it better.

Hope this would help you. You can get back to me, in case you need more help.

Regards,
Bagdevi Mishra.




2009/6/2 Eiichi AKAHO <akaho at pharm.kobegakuin.ac.jp>:
> Dear mishra:
>>  Have you tried castP from
>>  http://sts-fw.bioengr.uic.edu/castp/calculation.php
>
> I tried.
> Thanks for your help on my Q.
> By the way, I have a couple questions on CASPT. And I appreciate your help.
> 1. In the pocket column on the left, it says the volume and area of the pocket.
>  Please tell me the units of those numbers. Are they nanometer x 2, and x 3 or
> something else?
> 2. Are there any way to show the pocket with space-filled?
> 3. Are there any way to erase the other parts besides the pocket?
> Your help is greatly appreciated.
> Thanks in advance.
> Eiichi
>
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