From owner-chemistry _-at-_)ccl.net Mon Jan 30 20:37:01 2006 From: "Dr. Peter Bladon cbas25-$-strath.ac.uk" To: CCL Subject: CCL: suggestions for manual docking and building Message-Id: <-30713-060130195639-26786-pzT5OgVGz/sw5S9TD+XpSQ++server.ccl.net> X-Original-From: "Dr. Peter Bladon" Content-Type: multipart/alternative; boundary="------------090904010900080300060500" Date: Tue, 31 Jan 2006 00:50:17 +0000 MIME-Version: 1.0 Sent to CCL by: "Dr. Peter Bladon" [cbas25[A]strath.ac.uk] This is a multi-part message in MIME format. --------------090904010900080300060500 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Bruce Palfey brupalf|*|umich.edu wrote: >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 > > > Interchem-Pc has facilities for manual docking. It is free to academics. You would need the auxiliary program for converting PDB files to Interchem format. All of the Interprobe software is described on: http://www.interprobe.co.uk/inter/interprobe.html This website has a link to the site from where you can download the software. Peter Bladon Interprobe Chemical Services Gallowhill House, Larch Avenue Lenzie, Kirkintilloch Glasgow G66 4HX Scotland > > --------------090904010900080300060500 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit

Bruce Palfey brupalf|*|umich.edu wrote:

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

Interchem-Pc has facilities for manual docking. It is free to academics. You would need the auxiliary program for converting PDB files to Interchem format.

All of the Interprobe software is described on:

http://www.interprobe.co.uk/inter/interprobe.html

This website has a link to the site from where you can download the software.

Peter Bladon

Interprobe Chemical Services
Gallowhill House, Larch Avenue
Lenzie, Kirkintilloch
Glasgow G66 4HX
Scotland

 

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