Subject: Replies to my original post: Motif software or database?

From: Shaomeng Wang <[email-masked]>
Date: Fri, 11 Oct 1996 09:50:34 -0400

Dear CCL friends,

On Oct. 2, 96, I posted a message on the CCL about Motif searching 
software or database. I have received a number of replies to my question. I like to thank  
each of you for your time and information. Here is the collection of all
the replies.

******************************************************************************

If you have coordinates for a protein with an unknown motif,
try using Dali (http://www.embl-heidelberg.de/dali/dali.html).
That will give you the names of all proteins with similar
folds (and their motifs will probably be reported in the
literature).  Hope this is what you're looking for...

Jane

*******************************************
Jane Caldwell
Biophysics Program/Dept. Biochemistry
420 Henry Mall
University of Wisconsin-Madison
Madison, WI 53706

E-mail: [email-masked]
*******************************************
Hi,

You can find a list of available software for chemistry at:

http://laaksonen.csc.fi/docs/stuff.html

I hope this helps.

-- 
*************************************************
Istvan Enyedy
The Catholic University of America
Chemistry Department/ Malloney Hall
Washington DC 20064
email [email-masked]
phone 202-319-5707 or 5349
fax 202-319-5381
**************************************************
I vaguely remember that Prof. Janet Thornton published a series paper on 
protein motif and developed some software for this.

I believe Oxford Molecular Group markets her software under the name 
Idditis. Check their web site.

Shaomeng Wang wrote:
> 
> Dear CCL friends,
> 
> Could any provide me the information on the software/database for
> searching for known protein motifs?
> 
> I appreciate very much your information.
> 
> Shaomeng Wang, Ph.D.
> Georgetown University Medical Center
> 
> -------This is added Automatically by the Software--------
> -- Original Sender Envelope Address: [email-masked]
> -- Original Sender From: Address: [email-masked]
> [email-masked]: Everybody | [email-masked]: Coordinator
> [email-masked]: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73
> Anon. ftp: www.ccl.net   | [email-masked] -- archive search
>              Web: http://www.ccl.net/chemistry.html

-- 
Willie Cui, Ph.D.               voice: (201)512-0486
MicroSimulations                fax:   (201)512-0489
478 Green Mountain Road         [email-masked]
Mahwah, NJ 07430                http://www.microsimulations.com

The PDB has theoretical models which may be of help.
Professor David Eisenberg's group at UCLA would
definitely know: [email-masked] is a 
staff there and may know.  Tell him I sent ya.

AHSystems Group
"Your Work Just Got Easier!"

Contact Person:  John Parikh
5401 Lakeford Lane, Suite L-1, Bowie, MD 20720,=20
Phone (301) 352-0896, Fax (301) 352-0199, Web Site www2.ari.net/ahsystems,=
 E-Mail [email-masked]

Product Briefs:

HSC Chemistry for Windows (version 2.03)

HSC Chemistry for Windows is a chemical reaction and equilibrium  software=
 package which utilizes an extensive thermochemical database of over 7,600=
 compounds.  The program includes 7 different calculation options for=
 computing Gibbs free energies and equilibrium constants for reaction=
 equations, heat and material balances, equilibrium compositions, formula=
 weights, electrochemical cell equilibria, phase stability diagrams, and=
 Eh-pH (Pourbaix) diagrams.

Kinetics

Kinetics numerically integrates the rate equations for reversible multistep=
 chemical reactions to determine the concentrations of the chemical species=
 in the system as a function of time.  The program provides an easy to use=
 interface which allows users to create complex reaction systems by =
 entering the reactions of interest and the associated rate constants.  No=
 other input is required by the program. The program formulates the required=
 rate equations from the list of reactions. Graphical output of results can=
=20
be obtained, and an output file suitable for use in a spreadsheet program is=
 generated

TAPP

A Windows or Macintosh materials property database with thermophysical=
 property data for over 17,000 compounds and a collection of 1500 phase=
 diagrams.=20

TEP(Thermal Equilibrium Program)

TEP is an interactive chemical combustion analysis tool for assessing the=
 products of combustion under equilibrium conditions using the minimization=
 of the Gibbs free energy.  The NASA Lewis chemical equilibrium computer=
 program is used as the underlying solver.

HyperChem, ChemPlus, and HyperNMR

An extremely powerful molecular modeling package, HyperChem makes=
 computational chemistry more accessible to researchers and educators. =
 HyperChem is an integrated and flexible molecular modeling package that=
 offers a comprehensive set of tools for studying and predicting molecular=
 structures and properties.  The program includes a number of computational=
 options (geometry=20
optimization, molecular dynamics, etc.) utilizing several well known=
 molecular mechanics and semiempirical computational methods.

ChemPlus adds 9 extensions to HyperChem, including molecular rendering,=
 conformational searching, RMS overlap of molecules, sequence editing,=
 crystal and sugar building, and QSAR property calculations

HyperNMR calculates chemical shifts and coupling constants using quantum=
 mechanics and simulates the resulting NMR spectrum

PCModel

PCModel is an interactive molecular modeling program for the study of =
 organic and inorganic molecules on your personal computer or workstation. =
 The program contains the MMX force field for performing computations.=
 PCModel has many applications for organic chemists, biochemists and =
 educators.

-over-

MOPAC 6.0

Mopac is a general purpose semiempirical molecular orbital package for  the=
 study of chemical structures and reactions.  The program includes the MNDO,=
  AM1, PM3, and MINDO/3 Hamiltonians

Kekul=E9

Kekul=E9 for Windows and Mac provides unique technology for scanning and =
 automatically interpreting chemical structures.  The Windows version=
 includes a  full feature molecular editor, making this the most complete=
 molecular structure  input system available

PROCEDE for Windows

Procede is an easy to use process design programs which can be used to=
 creates engineering drawings and specification sheets. The program includes=
 a symbol library manager, allowing users to add custom symbols to=
 flowsheets. Custom equipment data can also be entered into specification=
 sheets.

OPTIMATR

OPTIMATR is a computer for calculating optical properties of materials.  A=
 database of optical properties is included for use during the  computations

TFCalc

TFCalc enables users to design and analyze optical thin film coatings.  =
 TFCalc computes the reflectance, transmittance, absorptance, phase-change, =
 electric field, and color of multilayer coatings consisting of dielectric=
 and  metallic materials

All products and trademarks are protected under appropriate laws and all=
 rights are reserved.=20

Special Bundle Offers

                Special Offer    Regular Price
                (Commercial/Academic)   (Commercial/Academic)
 AHS's ChemSuites=20
        HSC Chemistry / Kinetics / TAPP (BEST DEAL!)    $ 1280 / $1090  $ 1685 / $ 1485
        HSC Chemistry / Kinetics        $ 795 / $ 695   $ 1190 / $ 1090
        HSC Chemistry / TAPP    $ 995 / $ 895   $ 1090 / $ 990
        Kinetics / TAPP $ 695 / $ 595   $ 1090 / $ 890

        HyperChem 4.5 for Windows       $  2395/1195    $ 2595/ $ 1295
        HSC Chemistry for Windows (LOWEST $$$!) $ 580 / $ 580(2 user lic.)      $ 595 /=
 $ 595 (2 user lic.)
        Kinetics for Windows    $ 295 / $ 195   $ 595  /  $ 495
        TAPP (FREE upgrades for next 12 months) $ 450 / $ 395   $ 495  /  $ 395
        Cad Crystallography     $ 250 / $ 195   $ 349  /  $ 299=09
        TEP             $ 550 / $ 450   $ 795  /  $ 695
Shipping and handling charges not included in the prices.

AHSystems Group - 5401 Lakeford Lane, Suite L-1, Bowie, MD 20720 - Phone=
 301.352.0896 - Fax 301.352.0199

--=====================_844374534==_
Content-Type: text/plain; charset="us-ascii"

John Parikh
Marketing Manager
AHSystems Group
5401 Lakeford Lane, 
Suite L-1
Bowie, MD 20720
Phone 301.352.0896
Fax 301.352.0199
Web Site www2.ari.net/ahsystems

--=====================_844374534==_--
*

********************************************************************************