Subject: Packages for short peptide chains

From: Raistlin Majere <[email-masked]>
Date: Fri, 7 Apr 1995 16:41:31 +0800 (SST)

Hello,

  A few weeks ago I posted the following question:

   Anyone knows if there are good packages that use genetic algorithms or 
simulated annealing to determine minimum structures of small molecules
(ex: short peptide chains)?  I will post a summary of relevant replies.

  Unfortunately I did not receive many replies. However, I would like to 
thank all those who have so kindly replied my question :)

***** Message 1

From: [email-masked] (Bernhard Pabsch - Telekurs AG - FLCI)

Hi,

did you check out PEACS from the vanGunsteren (GROMOS) group?
They also hold another new algorithm which uses a list of 
visited conformational places.
Both are quite powerful new algorithms.

Cheers
Bernhard Anton Pabsch            Tel:   +41 (0) 1 279 23 02

***** Message 2

From: [email-masked] (Ed Jaeger)

In my previous position at Sterling Winthrop, I developed GA drivers
to both SYBYL and MACROMODEL's BATCHMIN to do conformational analysis
of small molecules.  I unfortunately do not have access to either of
these commercial modeling packages and hence I cannot provide you with
any specific solution but I can say that it has been done.

I look forward to other relevant responses.

Ed Jaeger      3-Dimensional Pharmaceuticals, Inc.	      ph:610-458-6052
[email-masked] 665 Stockton Drive, Suite 104, Exton, PA 19341 fx:610-458-8249

***** Message 3

From: [email-masked] (Joel Polowin)

>    Anyone knows if there are good packages that use genetic algorithms or 
> simulated annealing to determine minimum structures of small molecules
> (ex: short peptide chains)?  I will post a summary of relevant replies.

Our HyperChem software does simulated annealing; it also includes drawing
functions specifically for contruction of peptide chains.  The conformational
search module of ChemPlus might also be useful for determining minimum
structures of such molecules; it works by torsional variations.

Regards,
Joel

***** Message 4

From: [email-masked] (Harry C. Johnson)

Spartan 4.0 from Wavefunction Inc. has four new conformational
analysis methods, including a genetic algorithm and a Monte Carlo
approach.

For more information about Spartan, check out our web page at
http://wavefun.com.

-Harry

Best Regards,

 Loh Chang Shiung, 罗章雄  Internet e-mail: [email-masked] 
 Centre for Natural Products Research,      Contact no.: (65) 772 6872
 National University of Singapore.                       (65) 772 7816