Packages for short peptide chains
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: bernhard # - at - # F3.telekurs.ch (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: jaeger # - at - # 3dp.com (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
jaeger # - at - # 3dp.com 665 Stockton Drive, Suite 104, Exton, PA 19341
fx:610-458-8249
***** Message 3
From: polowin # - at - # hyper.hyper.com (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: hcj # - at - # mazda.wavefun.com (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, ~{B^UBP[~} Internet e-mail: mcblab43 # - at - #
leonis.nus.sg
Centre for Natural Products Research, Contact no.: (65) 772 6872
National University of Singapore. (65) 772 7816