ADL: Question

annalisa bordogna annalisa.bordogna at gmail.com
Mon Sep 27 23:46:37 PDT 2010


Hello,

why don't you try some protein-protein docking servers, instead?
For example:

- HADDOCK (http://haddock.chem.uu.nl/services/HADDOCK/haddock.php)
This is a protein-protein docking methods that requires some experimental
data (e.g. NOE, RDC, mutations or even interface prediction) in input. It
has several energy minimization cycles, thus treats the proteins as
flexible:

- ZDOCK (http://zdock.bu.edu/)
This is a FFT protein-protein docking method. It is very fast and complete
and it does not need any additional input data. To be like this, it treats
the proteins as rigid.

Hope it helps!

Cheers,
Annalisa

-------------------------------------------------
Annalisa Bordogna
PhD. Student
Università degli Studi di Milano - Bicocca
Milano - Italy
-------------------------------------------------

2010/9/28 Shradha Chopra Phd2009,BIC <shradha at nii.ac.in>

> Hi,
>
> Autodock is meant for protein small molecule docking. The number of torsion
> to be made flexible in Autodock is limited to 32. You can increase in by
> modifying the constant.h file (details available at
> http://mgldev.scripps.edu/pipermail/autodock/2009-January/004969.html).
> But
> increasing no. of torsions beyond 64 will exponentially increase the
> computing time.
>
> Best Regards,
>
> Shradha Chopra
> JRF
> BIC Lab
> National Institute of Immunology
> ________________________________________________
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>


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