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

You should go to a

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

3. TINKER Molecular Modeling Package The TINKER molecular modeling software is a 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 4.1 Major Release Date: June 2003 Last Minor Revision: September 22, 2003 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). Parameter sets for other standard force fields such as UFF, ENCAD and MM4 are under consideration. In addition, we are actively developing our own AMOEBA force field based upon polarizable atomic multipole electrostatics. Current Release The release of TINKER version 4.1 coincides with a new version 1.1 of the Force Field Explorer (FFE) visualization program and GUI. This major new release of FFE contains significant improvements over the initial 1.0 release: (1) bidirectional communication between TINKER and FFE is now via Java sockets, leading to much greater stability, (2) tighter integration with the TINKER programs, (3) improved graphics performance and speed, (4) many added features and improvements to the easy-of-use of the interface. Further information is available from the FFE web site linked below. Other changes from the previous TINKER 4.0 include new force field parameter sets, improvements to rigid body dynamics, a Nose-Hoover thermostat, 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 4.1 is neither backward nor forward compatible with earlier versions of TINKER. For example, earlier versions of parameter files should not be used with version 4.1 executables and vice versa.

4. Accelrys - Formerly MSI Molecular Simulations Inc. (MSI) was renamed Accelrys Inc. on June 1, 2001 of leading names in the molecular modeling industry to be the leading company MSI incorporated companies including http://www.msi.com/

@import url(/styles/about2002.css); /*IE and NN6x styles*/ CORPORATE OVERVIEW NEWSROOM EVENTS EMPLOYMENT ... CONSORTIA MEMBERS About Accelrys Corporate overview News room Events Employment ... About Accelrys Molecular Simulations Inc. is now Accelrys Molecular Simulations Inc. (MSI) was renamed Accelrys Inc. on June 1, 2001. Accelrys, the leader in simulation and informatics software for the pharmaceutical and chemicals process industries, was created from the combination of MSI, Oxford Molecular GCG , and Synopsys Accelrys homepage Accelrys launch press release MSI was the leading provider of simulation and modeling tools for drug discovery and chemical development. For full details of our simulation and modeling products see: Life Science Modeling and Simulation Materials Science Modeling and Simulation Molecular Simulations History Founded in 1984, MSI grew through the combination of a number of leading names in the molecular modeling industry to be the leading company in the area. MSI incorporated companies including BioDesign, Biosym, Polygen, Cambridge Molecular Design, and BioCAD. Many of these companies emerged from, or developed close links with, leading Universities Harvard, Cambridge, York and the California Institute of Technology are examples. The company's product-line included the best-known names in modeling for drug discovery: Insight, QUANTA/CHARMm, and Cerius2 as well as the unique tools for materials science modeling in the Cerius2 software environment, now available within Materials Studio.

5. Rasmol In Neuem Gewand Der Bericht beschreibt, welche neuen Funktionen in Rasmol 2.6AB implementiert wurden und beleuchtet ein wenig die Bedeutung und Entstehung des Programms. Beispielgrafiken deuten die F¤higkeiten des Programmes an und eine Linkliste weist den Weg zu weiteren RasMolSites. http://www.dkfz-heidelberg.de/spec/linux/rasmol/

Molecular Modeling mit RasMol von Andreas Bohne und Henryette Roth Der Bericht beschreibt, welche neuen Funktionen in Rasmol 2.6AB implementiert wurden und beleuchtet ein wenig die Bedeutung und Entstehung des Programms. Wie alles begann Wie es weitergeht Beliebt, weil benutzbar xmkmf make setzt das Programm dann zusammen. Neben ein paar #ifdefs im Code resultierte diese Manko durch die Vordefinition der Farbtiefe mittels eines typedefs . Da Rasmol in Bezug auf die Abarbeitungsgeschwindigkeit optimal programmiert wurde, bedeutet dies im Klartext, dass Pointer verwendet werden, und je nach typedef Rasmol und die Browser macro1.scr Andere Ansichten Autoren myemail("a.bohne") chemical/x-ras Rasmol (PDB/Expasy) chemical/x-pdb Eine PDB-Datei application/x-rasmol Rasmol (PDB German Mirror) application/x-spt Rasmol-Script chemical/x-gaussian-cube Gaussian Cube chemical/x-gaussian-input Gaussian Input chemical/x-mdl-tgf MDL Scretch chemical/x-mdl-rxnfile MDL RXN chemical/x-mdl-molfile MDL MOL chemical/x-jcamp-dx JCAMP-DX chemical/x-mopac-input MOPAC-Input chemical/x-xyz XMOL xyz-file Links 1) Rasmol 2.6AB (nur Unix)

6. Welcome To Hypercube, Inc. 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 Web Store What's New? Download Product Updates ... HyperChem 7.5 Now Shipping! Download and try the new OpenGL graphics with HyperChem 7.5 Evaluation! Read the announcement press release New STUDENT VERSION Now Available to Registered Students! Call 1-800-960-1871 or email for more information. Visit Our Scripts Page Did you know that HyperChem is scriptable? We are soliciting script contributions to post on our new Scripts Page! HyperChem Now Networks With Pocket HyperChem Pocket HyperChem Release 1.1 and HyperChem Release 7+ communicate! Run HyperChem on Your OS X Mac using Virtual PC Discuss HyperChem Hypercube now has an internet discussion group for HyperChem Release 7 and Molecular Modeling! Visit the site and share your comments with other users. Purchase HyperChem Lite Online Hypercube, Inc. is offering a fully electronic product downloadable from the World Wide Web. Press Release: HyperChem Release 7.5 Now Shipping

7. 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/

8. MathMol MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for those interested in the field of molecular modeling. 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).

9. Molecular ART Gallery molecular modeling Gallery. Polymers and Polymer Simulations. Dendrimers. Molecular Rheology Modeling flow and transport properties. Nanotechnology. http://www.wag.caltech.edu/gallery/art_gallery.html

Molecular Modeling Gallery Polymers and Polymer Simulations Dendrimers Proteins and Protein Simulations Molecular Rheology: Modeling flow and transport properties Nanotechnology Ceramics, Semiconductors, Alloys Quantum Chemistry and Electronic Structure Problems with this server should be reported to webmaster@www.wag.caltech.edu

10. Molecular Modeling Lernsystem molecular modeling der Arbeitsgruppe von Prof. Dr. Rainer Herges am Institut f¼r Organische Chemie der Universit¤t Kiel. http://scholle.oc.uni-kiel.de/herges/modeling/gliederung.html

Lernsystem Molecular Modeling MDL-Chime-Plugin Macromedia Shockwave START Autoren Lehrveranstaltung Vorlesung Molecular Modeling Erstelldatum seit Oktober 1998 Letzte Änderung am Download Modeling.zip (2.18 MB) TO/OL Lernumgebung

11. Molecular Modeling Heidelberg http://www.dkfz-heidelberg.de/spec/

Adresse Um unsere Seiten betrachten zu können, brauchen Sie eine Frame-fähigen Browser, For watching this pages you need a browser which can display frames. Pleas download : z.B. oder Internet Explorer 3.0+

12. Sdvlapp1 Software: Category: Molecular Modeling QUESTIONS. FEEDBACK. HOME. Employment. Events. Links. People. Programs. Publications. Support. Welcome. Category molecular modeling. Programs for the creation, manipulation and viewing of molecular http://www.msi.umn.edu/user_support/software/MolecularModeling.html

QUESTIONS FEEDBACK HOME Employment Events Links People Programs Publications Support Welcome Category: Molecular Modeling Programs for the creation, manipulation and viewing of molecular models. Amber Description AMBER: Assisted Model Building with Energy Refinement AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. Home Page http://www.amber.ucsf.edu/amber/ Tutorial Amber Tutorials Documentation Remote online documentation can be found on the Amber 6 Manuals and Amber 7 Manuals Local documentation in PDF and HTML format can be found in /usr/local/amber/amber6-serial/doc/ Setting Up Your Environment There are several versions of Amber: serial version, shared-memory parallel (multiprocessor) version (MP) and parallel version that uses MPI message-passing library. The MP version is only available on multi-processor SGI computers. The MPI version is available on SGI Origin computers. Note: Although serial and parallel versions share most of the code base, there are significant differences. In some cases, parallel version may not produce the same results as the serial version. The results for any new problem obtained with a parallel version should be carefully checked against the serial version. The two parallel verions, MP and MPI, are also significantly different from each other. The MP versions supports a richer set of features, but MPI version may provide better performance in certain cases. The MP version is generally more reliable. You must initialize your environment including default paths and environmental variables which the package uses to access the programs and associated files. To do this, enter the following commands:

13. Molecular Modeling Factsheet NCBI Resources. molecular modeling A METHOD FOR UNRAVELING PROTEIN STRUCTURE AND FUNCTION The molecular modeling Database. NCBI's molecular modeling DataBase (MMDB), an integral part http://www.ncbi.nlm.nih.gov/About/primer/molecularmod.html

National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Databases and Tools ... Site Map Science Primer: Bioinformatics Genome Mapping SNPs ESTs ... Phylogenetics Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources MOLECULAR MODELING: A METHOD FOR UNRAVELING PROTEIN STRUCTURE AND FUNCTION Proteins form our bodies and help direct its many systems. Proteins are fundamental components of all living cells. They exhibit an enormous amount of chemical and structural diversity, enabling them to carry out an extraordinarily diverse range of biological functions. Proteins help us digest our food, fight infections, control body chemistry, and in general, keep our bodies functioning smoothly. Scientists know that the critical feature of a protein is its ability to adopt the right shape for carrying out a particular function. But sometimes a protein twists into the wrong shape or has a missing part, preventing it from doing its job. Many diseases, such as Alzheimer's and "mad cow", are now known to result from proteins that have adopted an incorrect structure. Identifying a protein's shape, or

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

15. 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.

16. MATHMOL MODULES Concepts in Science through molecular modeling. Activities for Students and Teachers. Molecules of Life. Concepts in Mathematics through molecular modeling. http://www.nyu.edu/pages/mathmol/modules/modules.html

Concepts in Science through Molecular Modeling Activities for Students and Teachers The Properties of Water (student version) The Chemistry of Carbon Photosynthesis Molecules of Life Concepts in Mathematics through Molecular Modeling The 3-Dimensions of Mathematics and Molecules A Teacher's Guide to Building the Icosahedron as a Class Project Return to K-12 Mathmol Home Page

17. Computational Chemistry And Molecular Modeling Service f¼r die Berechnung von Molek¼lstrukturen und Molek¼leigenschaften sowie Erstellung von Molek¼lbildern. Es werden Beispiele gezeigt und die F¤higkeiten der verwendeten Programme erl¤utert. http://www.comchem.de/

Home deutsch english deutsch ... english Email: stefan@comchem.de Links modeling, modelling, computer, computational, chemistry, render, molecule, molecular, pictures, animation, picture, 3D, animations, VRML, pdb, Molekülbilder, Molekuelbilder, Bilder, Modell, Modelle, Molekuelmodelle, Molekülmodelle, Molekülmodell, Molekuelmodell, Molekuel, molekuel, Molekül, molekül, 3 D, räumlich, raeumlich, struktur, structure, Strukturen, Struktur, strukturen, Molekuelstruktur, molekuelstrukturen, Molekülstrukturen, molekülstrukturen, molecular, structures, organisch, organische, Chemie, chemie, chemistry, Chemistry, anorganische, Anorganische, Bio, bio, Computerbilder, Computergrafik, inorganic, organic, semi, empirisch, empirical, DFT, dft, abinitio, ab initio, Kraftfeld, Geometrie, optimierung, optimize, Computergrafik Service fuer Computerchemie - Molekuelbilder und Animationen. - Computational chemistry and molecular modelling service, Molekülbilder, Computergrafik, Art, chemical, molecular modeling, chemische Struktur

18. Journal Of Molecular Modeling Journal of molecular modeling. Probably the chemistry. You are looking for a good scientific journal in the field of molecular modeling? You 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

19. Biomimetic Chemistry And Molecular Recognition In Organic Synthesis Group Describes research areas, including the synthesis of biomimetic models of NADH and the molecular recognition of acids and amines. Also gives details on group members, lists recent publications and has information for applicants. http://biomimetic.crihan.fr

20. NCBI Structure Group MMDB, the molecular modeling Database, contains experimentally determined biopolymer structures obtained from the http://www.ncbi.nlm.nih.gov/Structure

PubMed Entrez BLAST OMIM ... Entrez Structure Search Entrez PubMed Protein Nucleotide Structure Genome Books Conserved Domains 3D-Domains GEO GEO Datasets Journals MeSH NCBI Web site OMIM PMC PopSet Taxonomy for What's New? MMDB NCBI's structure database 3D-structure viewer CDD Conserved Domain Database VAST Structure comparisons VAST Search Submit structure database searches PDBeast Taxonomy in MMDB Research Research topics and staff The NCBI Structure Group .. maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB, the Molecular Modeling Database, contains experimentally determined biopolymer structures obtained from the Protein Data Bank ( PDB Structure highlights MMDB now contains about 20,000 entries. They can be anything from short oligonucleotides or peptides to very large macromolecular complexes containing dozens of individual molecules. A more extensive description and help on using MMDB are available.. Text searches in MMDB (use the search toolbar at the top of this page) will yield Structure Query pages, providing access to entries that matched the keywords. Structure Summary pages for one/several/all of these may be retrieved. From the Structure Summary pages one may:

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