Subject: Molecular modelling software in education: SUMMARY

From: John Marelius <[email-masked]>
Date: Wed, 17 Mar 1999 09:01:58 +0100 (W. Europe Standard Time)

Dear CCL members,

I recieved a number of responses to my question about molecular modelling
software for educational use. Thanks to all who responded!

In summary, I was recommended the following software:

* Spartan by Wavefunction Inc., http://www.wavefun.com

* Hyperchem by Hypercube Inc., http://www.hyper.com

*  MOE - the Molecular Operating Environment by Chemical Computing Group, 
http://www.chemcomp.com

* MacroModel

* Sybyl by Tripos Inc., http://www.tripos.com

I was also referred to the "Resources of Protein Modeling" page at
http://compbio.ornl.gov/protein_group/resource/

John Marelius

+-----------------------------------------------------------------+
|          John Marelius                                          |
|          Dept. of Molecular Biology, Uppsala University         |
| E-mail:  [email-masked]                             |
| address: Box 590, S-751 24 Uppsala, Sweden                      |
+-----------------------------------------------------------------+

Here are the messages I got:

------------------------------------------------

From: "E. Lewars" <[email-masked]>
To: [email-masked]
Subject: PROGRAM FOR TEACHING

1999 March 10

Hello, Concerning your request for programs for teaching:
 I think the best one is Spartan. You could try the cheap, basic version
for
about $300, or the new, cmplete one (available about April) for $699.
 Spartan is made by Wavefunction, Inc. There are PC, Mac and UNIX
versions.
  Contact [email-masked] for more info'.

---------------------------------------------------

Date: Wed, 10 Mar 1999 13:29:04 -0500
From: Mathieu Roberge <[email-masked]>
To: John Marelius <[email-masked]>
Subject: Re: CCL:Molecular modelling software in education:
recommendations?

Dear Sir,

        Maybe you should have à look at the new versoin (5.1) of Hyperchem
>from Hypercube Inc. I think that it could do almost all you talked about.
There is a free demo on the Web site of Hypercube (witch works fine on
Windows NT):

http://www.hyper.com

The Laval University is using this software for an undergraduate course
for
almost six years now. You can have an idea of what is possible on this
course Web site:

http://www.chm.ulaval.ca/chm19380/

I must warn you that this site is in french...

Hope you'll find it interesting,

Mathieu Roberge

---------------------------------------------------

Date: Wed, 10 Mar 1999 15:13:59 -0500
From: Dong Xu <[email-masked]>
To: John Marelius <[email-masked]>
Subject: Re: CCL:Molecular modelling software in education:
recommendations?

Hi John,

You may check our "Resources of Protein Modeling" page at
http://compbio.ornl.gov/protein_group/resource/

Best regards,

-Dong Xu
 http://compbio.ornl.gov/~nxy

---------------------------------------------------

Date: Wed, 10 Mar 1999 14:15:39 -0500
From: Bill Hayden <[email-masked]>
To: John Marelius <[email-masked]>
Subject: RE: Molecular modelling software in education: recommendations?

Dear Dr. Marelius:

I noticed your request for software that you might use for teaching of
computational chemistry at your university.  I invite you to visit our web
site at:  http://www.chemcomp.com.

Our package, MOE - the Molecular Operating Environment, is the ideal tool
for an academic setting for both teaching and conducting research.

MOE has been written around an embedded language, SVL - Scientific Vector
Language.  Due to SVL, MOE gives users:
1. Out-of-the-box functionality:  all of our applications are built into
the
package.  These cover the whole spectrum of drug discovery including:  a)
Protein/Homology Modeling (complete sequence to structure), b) High
Throughput Discovery (Combichem and HTS Data Analysis), c) Traditiional
Modeling and Simulation and d)Methods Developement and Corporate
Deployment.
2. Source Code:  You recieve the actual source code for most of the
built-in
applications.  This allows you to change how the app looks (GUI) and how
it
works (algorithms).
3. SVL:  also included in the package is the SVL language that allows you
to
code up your own methods and ideas
In addition, we offer the only platform independent high-end software.
With
the package you recieve executables for:  SGI Unix, Sun, WinNT, Win95 and
DEC Alpha NT.

This unique marriage of architecture and platform independence makes MOE
ideal for deployment in a teaching environment where you are able to show
the students the fundementals of the methods as well as have them "look
under the hood" at the inner workings of the computations.

Once again, I invite you to visit our web page at:
http://www.chemcomp.com
and contact me should you like to try out a free 30 day evaluation of the
software.

Thanks,
Bill

William A. Hayden
Vice President
Chemical Computing Group
[email-masked]
http://www.chemcomp.com

---------------------------------------------------

Date: Wed, 10 Mar 1999 14:50:48 -0500 (EST)
From: "Prof. Robert Topper" <[email-masked]>
To: John Marelius <[email-masked]>
Cc: TOPPER ROBERT <[email-masked]>
Subject: Re: CCL:Molecular modelling software in education:
recommendations?

Hi,

Try PC SPARTAN Pro. I haven't used it, but I have
extensively used the UNIX and Mac versions of SPARTAN
in teaching my undergrads, as well as my research.
SPARTAN can build polypeptides, proteins, and nucleotides.
PC SPARTAN runs on WinNT, supposedly. It can do the visualization,
building and minimization tasks, as well as conformational
searching. It cannot do MD, though, but it will open up
a host of quantum methods as well as force-fields.
I'm not sure about the docking and scoring, but I think not.

See www.wavefun.com for more information. The prices are on
www.wavefun.com/software/multiplex/prodtables/prices.html

Hope this helps
best, rqt

---------------------------------------------------

Date: Thu, 11 Mar 1999 09:14:05 +0200
From: skwasnie <[email-masked]>
To: John Marelius <[email-masked]>
Subject: Re: CCL:Molecular modelling software in education:
recommendations?

Hi,

I can tell you of my somewhat limited experience with Hyperchem5.0 Pro.
I just went through that stage of looking for appropriate software myself,
so I can tell you that Hyperchem is quite nice, and not expensive (without
extra licences about 400$), but you can take a look at their homepage
www.hyper.com (homepage of hypercube). This will do, I think.
You can get a free trial for 30 days, as I recall, and the service is
quite
good. It runs under Win95/98/NT as well as Sun (but I'm not quite sure
of that last one). I hope you can use this information.

Serge Kwasniewski

---------------------------------------------------

Date: Fri, 12 Mar 1999 13:46:01 -0300 (BSC)
From: andre mauricio de oliveira <[email-masked]>
To: John Marelius <[email-masked]>
Subject: Re: CCL:Molecular modelling software in education:
recommendations?

Dear Prof. Marelius,
        In your case I think that programs MacroModel
([email-masked]) or Sybyl (http://www.tripos.com) are more
factible for your purpose.

Greetings.

---------------------------------------------------