[Dock-fans] Docking for a protein

Scott Brozell sbrozell at rci.rutgers.edu
Thu Nov 25 20:39:53 PST 2010


Hi,

Read and run the tutorials:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/index.htm

Note that peptides can have many rotatable bonds.  Read this and
its references:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#LigandFlexibility
But version 6.4 may have better performance:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#WhatsNewinDOCK6

scott

On Thu, Nov 25, 2010 at 12:40:12PM -0800, Mohiuddin Ovee wrote:
> 
> I am a newbie in docking field. I have an NMR structure of protein-peptide complex. Now, I want to use the structure for docking by DOCK 6.4. I'm reading the manual but it is so comprehensive that I am finding it difficult to use the manual efficiently.
> 
> Does anyone have the step-by-step instructions for docking using complex structure? If anyone can help me out with this, I'll be grateful. 
> 


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