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From: |
Barbara Murray <bmurray # - at - # jasper.uor.edu> |
Date: |
Tue, 01 Sep 1998 13:57:01 -0700 |
Subject: |
Summary: looking for molecular modeling program on web or free-long! |
Sometime ago I asked the following question and got many helpful
answers. I ended up using isis/draw and weblab viewer both free to
download. This is long
> Barbara Murray wrote:
>
> > I am part of a national committee running an undergraduate
> > pharmaceutical course on-line in the fall. We will be taking the
> > students through all the steps that are involved in getting a drug to
> > market. One of the things we want the students to do is to be able to
> > draw and look at their chosen molecule in some sort of modeling
> > program. Now, they don't really need to do calculations on this
> > molecule; just look at it and move it around. Calculations would only
> > be icing on the cake.
>
> Check out Chem3D at our website www.camsoft.com or www.chem3d.com. ChemOffice
Net 4.5 will allow you to sketch molecules in 2D using ChemDraw Net and build 3D
models (with a six heavy atom) limit using Chem3D Net. Chem3D Net will also
allow visualization (including surface visualization) of molecules stored in
various formats.
> Chem3D Std which is available at the student price of $79 allows model building
and 2D to 3D conversion and MM2 calculations.
> For more information checkout our web site or send email to info (+ at +)
camsoft.com
>
> Kam Chana
> CambridgeSoft Corporation
>
from wware()at()world.std.com
> I wrote a Java program that might do some of what you want. Because it's
> written in Java, you can run it on most browsers simply by visiting the
> web page at http://world.std.com/~wware/ncad.html.
>
> The thing it doesn't do is to load and save molecule files (e.g. PDBs)
> from your machine. Partly this is my laziness, and partly it's the Java
> security model. But if you express interest, I might get motivated to
> put in a load/save feature.
> Your recent message to the CCL about the on-line pharmaceutical course you
> are running was forwarded on to me.
>
> In looking for desktop modeling software, I would like to invite you to
> consider the WebLab ViewerPro, Molecular Simulation's desktop 3D chemical
> visualization software program. The WebLab Viewer a member of a suite of
> products designed to enable chemical modeling, simulation, and
> visualization on the web.
>
> As a native desktop software program, the ViewerPro works as a browser
> helper application that will allow for the visualization, manipulation,
> and
> analysis of chemical structures accessed on the Internet. In addition to
> reading a wide range of file formats, the ViewerPro includes tools for
> sketching molecular structures. It is also integrated with the most
> popular 2D drawing packages, allowing the user to convert a 2D sketch into
> a 3D structure with a simple cut and paste.
>
> At your earliest convenience, please give me a call or drop me a note. I
> would appreciate the opportunity to discuss how the Viewer, and perhaps
> other MSI solutions, might assist you in your efforts.
>
> I look forward to hearing from you.
>
> Sincerely,
>
> John Wintersteen
> Product Manager, WebLab Viewer Products
> Molecular Simulations Inc.
> 9685 Scranton Road
> San Diego, CA 92121-3752
> 619-799-5791
> http://www.msi.com/viewer
>
> Here are some sites with molecular modelling programs-some for
> free, some you have to purchase:
>
> http://world.std.com/%7Ewware/ncad.html
> http://www.carol.com/mass.shtml
> http://www.gaussian.com/
>
> Some sites containing information on aspects of computers-
> chemical reactions.
>
> http://chemistry.gsu.edu/post_docs/koen/wsoftwar.html
> http://www.digichem.co.uk/msover.html
>
> Computer-assisted synthesis planning
> http://www.caos.kun.nl/
> http://www.shef.ac.uk/~chem/chemdex/computational.html
>
> Combinatorial chemistry
>
> http://www.msi.com/corp/pdf/c2_builder_modules.pdf
>
> Let me know how you get on.
>
> Dr Andrew Czarn
> Nanotechnologist
>
>
> I can't help you with your specific questions, but the CMS Molecular
> Biology Resource web site at http://www.sdsc.edu/ResTools/ should be
> useful to you.
>
> It is a compendium of electronic and Internet-accessible tools and
> resources for Molecular Biology, Biotechnology, Molecular Evolution,
> Biochemistry, and Biomolecular Modeling.
>
> This was recently reviewed (July 10) in the NetWatch column of
> _Science_, the weekly publication of the American Association for the
> Advancement of Science:
>
> The site is a functional listing of public-domain Web tools
> in the domain of molecular biology. "The 1900 or so links
> here are organized according to the task at hand, whether
> it's identifying a protein based on its peptide fragment map,
> scouring a gene for coding regions, predicting a protein's
> 3D structure, or doing a phylogenetic analysis," writes the
> NetWatch column's editor, Jocelyn Kaiser.
>
> As Chris explains at the site, he began collecting these
> resources and organizing them in this way in 1995, while he
> was in the Department of Biochemistry at the University of
> Nebraska, Lincoln. It has been updated five times, with the
> latest update occurring after Chris came to SDSC in June 1996.
> The site is mirrored at 11 sites around the world.
>
> Molecular Science is one of SDSC's "Thrust Areas".
>
> - Wayne Schroeder -
> San Diego Supercomputer Center
> http://www.sdsc.edu/~schroede
>
from dough $#at#$ mdli.com
> I would recommend ISIS/Draw to draw in structures, then transfer molfiles
> to MSI's Weblab viewer, will pop them into 3D and display in a highly
> interactive manner, including surfaces. Both ISIS Draw and Weblab viewer
> lite are available free on the web.
>
> Hello,
>
> over the last year i have also been trying to find a free/cheap
> modeling program for structure visualization etc. the only free program
> I found is Molgen, however, it is DOS based and difficult to use. the
> solution i have settled on is ChemSite. the price is about $100 per
> copy but it decreases when a large number of copies are purchased.
> concerning ease of use, it is not as intuitive as i would like, but it
> is fairly straight forward to build a structure, minimize it and then
> view it. the web site is
>
> http://www.webcom.com/molvis/
>
> as part of the course i teach i have developed a de novo drug design
> lab which is based on a simplified receptor; the receptor is an actual
> chemical, however, it is very 2D in nature and, thus, easy to analyze.
> if you are intereted i would be happy to send you more info.
>
> alex
>
> --
> Alex MacKerell, Ph.D.
> Associate Professor
> School of Pharmacy
> University of Maryland
> 20 North Pine Street
> Baltimore, MD 21201
> 410-706-7442
> 410-706-0346 (fax)
>
> alex # - at - # mmiris.ab.umd.edu or
> alex : at : rx.umaryland.edu
> http://www.pharmacy.ab.umd.edu/~alex/
>
from snmjohnson at.at iclub.org
> I find ISIS/Draw to be pretty useful for generating 2D & 3D structures.
> It will
> allow you to create a 2D structure which can be exported & inserted into
> Word
> documents and such, and as far as the 3D stuff goes, after you make your
> 2D
> diagram, you can then view the structure with RasMol.
>
> Oh yeah, and it's free. :)
>
> You can find it at the following location:
>
> http://www.mdli.com/download/idrawdown.html
>
>
> Sean Johnson
> Barbara-
> I too have been looking for a "free" program for building
> molecules.
> Unfortunately there is none that is currently supported. There was a
> program called Molden that is free, but I tried to download it and install
> it, and the installation failed. Searching for Molden on www might get
> you
> there. It may also be referred to in the ccl archive. There is also a
> site
> that will build it for you as I understand, but that is not satisfying for
> a
> course. Alas I do not know the address for this site.
> The cheapest molecule building programs that give you 3D viewable
> molecules in formats that can be either directly output to PDB format or
> easily converted are Spartan (Mac or PC) and HyperChem-"Chemlite" actually
> (PC only). The prices are $300 and $150 respectively. Chemlite also
> sells
> for around $70 for students. Spartan has a more powerful builder with
> templates and the $300 version (there is a more powerful version for $445)
> would be excellent for your class. Unfortunately, $300 is a tough pill
> for
> an undergrad to swallow. Spartan can export to PDB format. Chemlite does
> not and you would have to use Babelwin if you want your students to view
> their molecules with chime or rasmol. $70 is about the cost of a
> textbook.
> Chemlite/Hyperchem's builder is by far easier for students to learn, so if
> you are looking for a quick return for your students, Chemlite is your
> program. By the way, with both of these programs you get molecular
> mechanics, and with Spartan you get Quantum mechanical optimizations too.
> Chemlite has a nonoptimizing extended huckel module.
> Finally, there is a program called Sculpt, but it is >$500 as I
> recall. It is a good program an has a good builder module.
>
> If you figure something out, please let me know. I would be happy
> to follow up on anything I have said here. Good luck!
>
>
> Cheers,
>
> Jim
>
> James M. Lo Bue
> Assistant Professor of Chemistry
> Georgia Southern University
> P. O. Box 8064
> Statesboro, GA 30460
> Ph: 912-681-0398 Fax: 912-681-0699
>
>
from adam;at;cherwell.com
> Barbara
>
> Take a look at ChemSymphony:
>
> http://www.chemsymphony.com/
>
> You will be particularly interested in the Extranet section and the
> example
> of well known drugs in the gallery
>
> http://www.chemsymphony.com/gallery/pharmas/index.html
>
> ChemSymphony Beans is a toolkit. You could use our 3D sketcher (see the
> MOPAC example) to do this. But note that ChemSymphony Beans is a toolkit
> so
> you would need to invest some time in building the site to do exactly what
> you want. It sounds quite ambitious to me (I mean the expectation of your
> students are quite high)!
>
> I will be interested ot learn how you decide to do this.
>
> Regards
>
> Adam
>
>
>
> Chemsymphony is everything you ask for and more (it does
> optimisations via MOPAC). It can be found at
>
> www.chemsymphony.com
>
> It is totally web based with molecules drawn online, calculations
> submitted an results retreived back into the applet. Check out
> the "extranet" section.
>
> Regards
> Carl
>
> P.S. I have no affiliation with the company
>
> ---------------------------------------------------------------
> |E-mail for life: carl.windsor()at()bigfoot.com |
> --
>
> Barbara,
>
> Its not really what you're looking for, but in a (local) course that I run
> here at Bradford, students use ISIS Draw (free and downloadable) to draw
> 2D structures and then cut-and-paste these into MSI's WebLabViewer
> (free and downloadable) to display, rotate, etc in 3D. It's all simple
> stuff that we do - but one of our aims is to get the students to
> draw molecules using 2D drawing packages as well. In your case this
> means getting the students to download 2 pieces of software - probably
> not ideal - and construction of the molecules occurs in 2D rather than
> 3D.
>
> If you come across any free JAVA-based packages that allow construction
> of molecules in 3D I'd love to hear about them.
>
> Regards,
>
> Steve
>
> // Email : S.W.Doughty;at;bradford.ac.uk \\
> // WWW : http://abbot.pharm.brad.ac.uk/
\\
> ----------------------------------------------------------------
>
>
> May I suggest you look at these two options:
> 1 - Molecules-3D (v2.5) a very inexpensive 3D model building program ($49
> student
> price)
> http://www.molecules.com/m3d_sefs.htm
> 2 - WebMolecules - an online VRML-based visualization Library (plug-in
> req'd)
> http://www.molecules.com/vrmlmols/index.html
>
>
> --
> David Segrist
> Molecular Arts Technical Support
>
> ----------------------------------------------------------------
> Molecular Arts Corporation |
> Hanover Corporate Centre, Suite 1000 | http://www.molecules.com
> 1532 East Katella Avenue | Main: (714) 634-8100
> Anaheim, California 92805-6627 USA | FAX: (714) 634-1999
> ----------------------------------------------------------------
>
from haun "at@at" intsim.com
> HI Dr. Murray,
>
> I would suggest that you have a look at our software, SCULPT. SCULPT
> allows you to take a structure, view it in 3D. In addition, it is
> equippied with some very simple toolsdriven by a mouse; it allows you to
> bend and twist portions of the structure while simultaneously giving you
> visual feedback on steric forces. It uses Amber and UFF for
> minimizations.
> This is great for exploring secondary structures and receptor sites. If
> your focus will be on small structures, it allows the user to
> superposition
> flexible structures for conformational analyses. It is a great tool for
> students and more professional chemists and biochemists.
>
> For file compatibility it reads: PDB, MDL Mol (copies and pastes from ISIS
> Draw), and (copies and pastes) CS Chem3D files. Thus it supports, ISIS,
> ChemWindows, CS Office. The new beta version 2.6 for Windows also has hot
> linking capabilities with MDL's Chime, beta 2.0. Incidentally, this
> version of Chime also has a sculpting function to it - choose the right
> button on the mouse.
>
> We also offer a great 3D builder called ChemBuilder3D which allows the
> user
> to build small molecules by a fragment library. It also has MM3 and UFF
> and allows you to change torsion angles and conformations (cis to trans)
>
> If you are interested, please contact me and/or visit our web site
> http://www.intsim.com for more information
and a free trial.
>
> Best regards,
>
> Dan Haun
>
--
***********************************************************************
Barbara Murray bmurray #*at*# uor.edu
Chemistry Department 909-793-2121 ext 2374
University of Redlands FAX 909-793-2029
1200 E Colton, PO Box 3080
Redlands, CA 92373-0999
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