1. TINKER Molecular Modeling Package Complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. http://dasher.wustl.edu/tinker/

TINKER Home Page TINKER - Software Tools for Molecular Design Current Major Version: TINKER 4.2 Major Release Date: June 2004 Last Minor Revision: September 8, 2004 Introduction The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. TINKER has the ability to use any of several common parameter sets, such as Amber (ff94, ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000), OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L), Liam Dang's polarizable potentials, and our own AMOEBA polarizable atomic multipole force field. Parameter sets for other standard force fields such as GROMOS, UFF, ENCAD and MM4 are under consideration for future releases. Current Release The release of TINKER version 4.2 coincides with a greatly improved version of the Force Field Explorer (FFE) visualization program and GUI. This major new release of FFE contains significant improvements in many areas such as stability, feature set and integration with TINKER. Further information is available from the FFE web site linked below. Other changes from the last TINKER version include the initial public release of a complete AMOEBA protein force field parameter set, and numerous minor additions and bug fixes, many of them suggested by users of the package. Please note that as with prior new releases, version 4.2 is neither backward nor forward compatible with earlier versions of TINKER. For example, earlier versions of parameter files should not be used with version 4.2 executables and vice versa.

2. Molecular Modeling Home Page Links to information on chemical structures, graphics, slide shows, and modeling experiments. http://www.molecules.org/

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3. Center For Molecular Modeling Center for molecular modeling Several tutorials related to molecular modeling, directory of software and links to databases. http://cmm.info.nih.gov/modeling/

4. MathMol Provides students, teachers and researchers the basic concepts in mathematics and their connection to molecular modeling. Links to Software, 3D libraries http://www.nyu.edu/pages/mathmol/

MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for those interested in the field of molecular modeling. Hypermedia Textbook( Version2) New Introduction to molecular modeling for middle and high school students. This updated version contains java applets, Flash movies and javascript interactive activities. The MathMol Tutorials have been updated to work using JavaMage so they can be performed online. K-12 Chime Tutorial New A Chime tutorial designed for middle and high school students. The tutorial can easily be adapted for high er level use. Quick Tour What is molecular modeling? Why is molecular modeling important? Why the math in MathMol? This link contains numerous images and MPEG files. More about MathMol Where is MathMol being developed? What are the objectives of MathMol? Why is this site so important to education? Public Domain Software What is the latest public domain software available for PC's, Mac's and Unix workstations? Where can this software be obtained? (Software found here can be used to read all the files in the the MathMol Library.) Library of 3-D Molecular Structures The MathMol Library of Molecular Structures contains GIF, PDB and 3-D (VRML) files of molecules that are found in most introductory biology and chemistry textbooks (e.g., water and ice, carbon, hydrocarbons, amino acids, nucleotides, lipids, sugars, photosynthetic pigments and drugs).

5. Center For Molecular Modeling Center for molecular modeling Several tutorials related to molecular modeling, directory of software and links to databases. http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

6. Center For Molecular Modeling http://cmm.info.nih.gov/

7. MolMo Services: A Molecular Modeling And Drug Design Company Software for chemoinformatics, bioinformatics, and drug design; consulting services for the chemical and pharmaceutical industry. http://www.molmo.be

Home About Services Software ... Publications MolMo Services provides a wide range of computational research services for the chemical and pharmaceutical industry. We offer our customers dedicated software for the most demanding challenges in computational chemistry and data-processing. We can also offer a modern facility for contract-based computational research, where our highly qualified and experienced team will produce the right solution for your computational needs. For an overview of the software we have developed in the past, we suggest you take a look at the software page and at some applications of our software in the field of molecular modeling and drug design.

8. Molecular Library Library of 3D Molecular Structures http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

9. Molecular Modelling Summary of lecture course which aims to introduce the hierarchy of computational modeling methods used in Organic Chemistry. Links to background and supplemental information. http://origin.ch.ic.ac.uk/local/organic/mod/

c) Henry Rzepa. 1995-2003.

10. MathMol Provides students, teachers and researchers the basic concepts in mathematics and their connection to molecular modeling. Links to Software, 3D http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

11. Molecular Modeling Home Page molecular modeling was introduced at Lebanon Valley College through support by The Chemistry Department built a molecular modeling Laboratory housing 10 http://www.molecules.org/index_noframes.html

Frames version Molecular Modeling for Chemical Education Chemical Structures Workshops Record of ... Other Sites Summary of Activities at Lebanon Valley College Molecular modeling was introduced at Lebanon Valley College through support by the College and a $49,188 grant titled "Molecular Modeling Throughout the Chemistry Curriculum" from the National Science Foundation. The Chemistry Department built a Molecular Modeling Laboratory housing 10 Power Macintosh computers (233-MHz G3, 64 MB Ram, 4 GB hard drive, internal ZIP drive, 24X CD-ROM) which run CAChe Scientific software and a Silicon Graphics Indigo II Workstation running Tripos software. Another grant from the National Science Foundation "A Consortium for Molecular Modeling Using Workshops and the World Wide Web" supports workshops for undergraduate faculty . This web site has grown from the activities under these grants. Please browse the site using the links given toward the top of the page. We would like to have your comments and suggestions, so please let us know you were here and give us feedback A Slide Show describes uses for molecular modeling.

12. MEDIT - Home - Molecular Extended Distribution In Information Technology - Http: French company working on software development and services in bioinformatics, cheminformatics and molecular modeling. Offers insilico services for R D in pharmaceutical, cosmetic, agrochemical, and biotechnology industries. http://www.medit.fr

About MEDIT Products Services News About MEDIT Products Services News ... Contact us

13. Representation Models In Molecular Graphics The Representation of Molecular Models http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

14. B Home Page B (formerly known as Biomer) is a Javabased molecular modeling program for small organic molecules and biopolymers. Supports nucleic acids (DNA/RNA), polypeptides, polysaccharides, the AMBER force field, geometry optimization, simulated annealing. Exports jpeg, gif, and ppm images. http://www.scripps.edu/case/Biomer/

15. Molecules From Chemistry At Okanagan University College Information on molecular fragments with pictures of the molecular models of various functional groups including alkanes, ketones, and alcohols. http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

16. RasMol Home Page Molecular visualization freeware for proteins, DNA, and macromolecules. Freely available for Windows, Macintosh, and UNIX. http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

17. Journal Of Molecular Modeling The Journal of molecular modeling is the first journal in chemistry to offer network, print based and CDROM editions. The Journal is fully citeable with http://www.ccc.uni-erlangen.de/jmolmod/

Journal of Molecular Modeling Probably the most successful electronic journal in chemistry You are looking for a good scientific journal in the field of molecular modeling? You want brand new information about today's current topics? You think that color graphics and 3D-data files should be part of an innovative publication? But you also like classical printed journals? Then give the Journal of Molecular Modeling a try. Don't miss taking a look at our list of abstracts of published papers. The Journal of Molecular Modeling is the first journal in chemistry to offer network, print based and CD-ROM editions. The Journal is fully citeable with CAS-abstract, ISI-entry and ISSN (0948-5023). The final product is produced and distributed by the Springer-Verlag. If you want to keep pace with leading-edge research in the field of molecular modeling and experience the rapid development of scientific publishing, the Journal of Molecular Modeling is a must for you. You make this Journal a success! Become an author in the Journal of Molecular Modeling Last change: 26/03/2003 by Webmaster

18. MoluCAD Educational software for chemistry students, for the creation and visualization of complex molecular structures in 3D. Demo and online purchasing available. http://www.molucad.com/molucad/index.htm

MoluCAD ...a molecular modeling and visualization tool MoluCAD is a full-featured molecular modeling and visualization tool designed for Windows. Originally conceived as an aid for students of organic chemistry, MoluCAD has quickly evolved into much more. The latest version incorporates many advanced features only found in expensive workstation-based modeling packages. Ease of use, premium graphical quality, and computational robustness are the trademarks of MoluCAD. Novice users are able to quickly generate models, view them form any perspective, create reaction animations, and save all data to disk. MoluCAD is distributed by download from this website. [Download MoluCAD Demo] Easily Model Structures in True 3D Build Reaction Animations Easily Examples: EAS Diels-Alder Cyclohexane-Flip Interactive Periodic Table HTML-Based Help Built-In MM2 Energy Minimization MoluCAD is the result of a 3-year National Institutes of Health biomedical technology research project aimed at producing low-cost educational software for chemistry students. See the December 1997 NCRR Reporter article, "

19. Welcome To Hypercube: 20 Years Of Molecular Modeling & Computational Chemistry Producer of HyperChem, a molecular modeling package for windows and HyperNMR, a program for prediction of onedimensional NMR spectra. http://www.hyper.com/

Contact Us Visit our online Retailer of Chemistry Software What's New? Downloads ... MolecularModeling.com Now Recruiting Beta Testers : HyperChem for the MAC Hypercube would like thank all of the Beta testers for contributing valuable feedback with Beta1. We will be releasing Beta 2 shortly. Please check back often for updates. NEWS HyperChem 7.52 Update Available Hypercube Receives Phase II NIH-STTR Funding HyperChem 7.5 Now Shipping! ... [Home] 1115 NW 4th Street, Gainesville, FL 32601 USA Phone (352) 371-7744 Fax (352) 371-3662 email

20. Welcome To Hypercube 20 Years Of Molecular Modeling Producer of HyperChem, a molecular modeling package for windows and HyperNMR, a program for prediction of onedimensional NMR spectra. http://tmsyn.wc.ask.com/r?t=an&s=hb&uid=24312681243126812&sid=343126

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