From owner-chemistry@ccl.net Mon Jan 30 02:25:00 2006
From: "Kalju Kahn kalju(a)chem.ucsb.edu" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: suggestions for manual docking and building
Message-Id: <-30693-060130004602-29084-pHDsReG8D4F4ySgQbhdLdQ%%server.ccl.net>
X-Original-From: Kalju Kahn <kalju-*-chem.ucsb.edu>
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Date: Sun, 29 Jan 2006 21:45:53 -0800
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Sent to CCL by: Kalju Kahn [kalju__chem.ucsb.edu]
Dear Bruce, 

I have found SYBYL useful for such tasks.  It lacks some of your ideal
characteristics (not free, not Windows PC) but it is:

-direct.  You can mouse-maneuver easily the ligand or the protein or
both via intuitive global/local control toolbox.  

-easy loading.  Separate PDB files are loaded into different
overlapping molecular areas.  Once docked, the coordinates can be
merged and written out as a new PDB file.

-intuitive.  While SYBYL is not the easiest program to grasp, the
manual docking is very intuitive.  Ability to easily
display/hide/delete/color-code parts of the system help (e.g. hide all
but the residues within 6 A of active site is helpful).

-cheap platform that supports hardware stereo could be an used SGI
workstation or a newer Linux PC.  In practice, the docking can be done
reasonably well without 3D stereo.  

-the academic pricing for the SYBYL Base is reasonable if you find the
program useful for general modeling as well.

If cost is your main criterion, PyMOL might be a good candidate but I
had harder time figuring out how to perform manual docking with it.

Best wishes, 

Kalju  

-------------------
> Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
> Hi
> 
> I was wondering if people could suggest a good program for manually 

> and interactively building protein-ligand or nucleic acid-ligand  
> complexes.  Characteristics of the ideal program are:
> 
> - Direct.  I'd like to be able to grab one molecule and maneuver it 

> into a position I think is interesting using simple, direct mouse
and/ 
> or keyboard controls.
> 
> - Easily loaded.  The molecules - either macro or micro - would most
 
> likely come from different pdb files, though support of other
formats  
> would also be helpful.  A minimum of file preparation/conversion is 

> desirable.
> 
> - Intuitive.  The students who pass through my lab should be able to
 
> just pick it up and go; we need a tool to support our research,  
> rather than a system to dedicate our efforts to mastering.
> 
> - Available for common cheap platforms.  I'd like to use this on
PC's  
> in my lab or on my Mac laptop, or both.
> 
> - Supports hardware stereo.  It seems to me that that's the best way
 
> to build.
> 
> - Free.  Or cheap.  Or at least a good value worthy of an
investment.
> 
> I welcome all suggestions, and will summarize what I learn.
> 
> ciao,
> Bruce Palfey
> Department of Biological Chemistry
> University of Michigan Medical School
> Ann Arbor, MI 48109-0606> 
>
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara