ADL: Blind docking or local docking

vadiraj kurdekar vadirajgcppc at yahoo.co.in
Fri Feb 14 03:45:44 PST 2014


Hi Hemendra

you are performing blind docking. you may end up with wrong results. identify binding pockets based on literatures or cocrystalized ligands or by using active site prediction softwares like 
1. DoGSiteScorer: Active Site Prediction and Analysis Server http://dogsite.zbh.uni-hamburg.de/
2. http://bioinformatics.cm-uj.krakow.pl/activesite/
3. http://proline.physics.iisc.ernet.in/pocketdepth/

With Regards,
 
Vadiraj Kurdekar,
Research Scholar, Pharmacy Dept.,
Birla Institute of Technology and Science-Pilani,
Pilani Campus, 
Rajasthan, PIN: 333031
India.
Mobile: + 91 9460763664

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On Friday, 14 February 2014 9:39 AM, Hemendra Pal Singh Dhaked <hemendrapsd at gmail.com> wrote:
  
Dear all
i am using AutoDock4.2. i have large size of protein for docking. To cover
entire surface of protein if i increase the of grid size upto 170 *170*170
with grid spacing of 0.375. such docking will be Blind docking or local
docking.
please tell me.

Thanks
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