CCL: suggestions for manual docking and building

 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