[Dock-fans] Free docking programs for windows

John J. Irwin jji at cgl.ucsf.edu
Fri Jul 25 10:44:57 PDT 2008


Hi Ruhul

If you can get the source, you should be able to get most docking 
programs to run on Windows, under cygwin. For instance, to make DOCK on 
windows, please refer to our wiki. 
http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_on_cygwin

DOCK is free to academics, and will run happily on Windows, under Cygwin.

As you know, there are many docking programs to choose from, and 
different people have different views. Writing to dock-fans, one should 
not expect an unbias opinion. One way to get an idea of which docking 
programs might work best for you is to use the literature. There are 
many papers that attempt to compare docking programs, but a good place 
might be Warren (below). Next, look for papers that report the discovery 
of novel ligands (if that is what you are interested in), paying 
particular attention to those that report crystal structures.  A review 
that mentions some of these is Shoichet, below.

Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, 
Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven 
JM, Peishoff CE, Head MS. 
<http://www.ncbi.nlm.nih.gov/pubmed/17004707?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> 
<http://www.ncbi.nlm.nih.gov/pubmed/17004707?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> 

A critical assessment of docking programs and scoring functions.
J Med Chem. 2006 Oct 5;49(20):5912-31.


Shoichet BK. 
<http://www.ncbi.nlm.nih.gov/pubmed/15602552?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> 
<http://www.ncbi.nlm.nih.gov/pubmed/15602552?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum> 

Virtual screening of chemical libraries.
Nature. 2004 Dec 16;432(7019):862-5. Review.

Good docking!

John
UCSF DOCK Team


Ruhul Amin wrote:
> Hi,
>
> Can anyone tell me please which docking programs are better that runs 
> on windows xp and free for academic users?
>
> Thank you,
>
> Ruhul
>
>


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