1. Center For Molecular Modeling Center for molecular modeling Several tutorials related to molecular modeling, directory of software Category Science Chemistry Computational...... http://cmm.info.nih.gov/modeling/

2. Accelrys - Formerly MSI Develops modeling and visualization software for researchers in materials science and the life sciences. Download trial versions. the combination of a number of leading names in the molecular modeling industry to be the leading company in the area. 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.

3. MathMol Instructional materials related to the use of molecular modeling in the undergraduate chemistry curriculum molecular modeling was introduced at Lebanon Valley College through support by the College and a $49 188 grant titled 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. 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). Water Module This site contains background information on water and ice, MPEG files of computer simulations of water molecules in motion, and water and ice databases.

4. Journal Of Molecular Modeling German journal presents papers on computeraided modeling, using color, and 3D images. View the table of contents and abstracts. Journal of molecular modeling. Probably the most successful electronic journal in chemistry 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 on the molecular modeling field? You want brand new information about todays current topics? You expect an electronic journal to be a serious publication? 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 to have a look at our list of abstracts of published papers and feel free to get your personal copy of selected 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). Dont't hesitate: here is your opportunity to compare three different presentation technologies and to get insight into the impact the WWW is going to have upon your daily scientific work. 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.

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

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

PubMed BLAST OMIM Taxonomy ... Entrez Structure Search Entrez PubMed Protein Nucleotide Structure Conserved Domains 3D-Domains Genome PopSet Taxonomy OMIM 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 Semi-automated annotation of taxonomic sources in MMDB has resulted in taxonomy links for about 38.000 molecules with 3D structure information. This allows for organism-based queries in Entrez's structure division. More.. Text searches in MMDB (use the search toolbar at the top of this page) will yield Structure Query pages, providing access to entries which matched the keywords.

7. Springer LINK: Journal Of Molecular Modeling - Contents Molecular, protein, peptide and drug design, computational modeling, molecular mechanics/dynamics Category Science Biology Publications Journals Fulltext J......Springer LINK, Forum Springer Journal of molecular modeling. ForumWhat's New Search Orders Helpdesk Up. Online First 2003 9/1, 2002 http://link.springer.de/link/service/journals/00894/tocs.htm

TM Example of a published paper in HTML and PDF format Example of a protein structure available in the journal Last update: 14 March 2003 LINK Helpdesk

8. Representation Models In Molecular Graphics Concepts in Science through molecular modeling Activities for Students and Teachers Concepts in Mathematics through molecular modeling http://scsg9.unige.ch/fln/eng/toc.html

The Representation of Molecular Models Rendering Techniques Part I The Representation of Molecular Models Part II Rendering Techniques. This page has been accessed times since the 1rst January 1995 (after six months accessibilty) thank you very much for your interest. Part I 1. Structural models. 1.1 The wire-frame model. 1.3 The space-filling model. 1.4 The stick model. ... 7. Future. Part II 1. Shading techniques. 1.1 Classical illumination model of a polygon mesh 1.2 Shading : 1.2.1 Constant shading. ... Chemistry on the Internet: The best of the Web 1995! Other local servers Same document in French Have a look at the public defense of my Ph. D Crystal in Europe University of Geneva FTP access to the SGI file format images of the current document New All the gif images used in theses documents! Table 1 Table 2 Servers list dealing with chemistry francois.savary@chiphy.unige.ch ... Bridge BCC Group of Professor J. Weber, Department of Physical Chemistry, University of Geneva 30, quai Ernest Ansermet CH-1211 Geneva 4 tél.: +4122 702 65 32

9. 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)

10. 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/

What's New? Hardware Lock Licensing for Release 7 P urchase a Product Online! Products, Free Software and Demos Novell Server? Please Read This Page First Product Updates ... And the Winner of the Third Annual Hypercube Classic Golf Tournament is.... The tournament was held at the Sanibel Symposium, Wednesday, February 26, 2003 Special Upgrade Pricing for Release 5 and Lower! Special Pricing Extended Until March 31, 2003!! Upgrade from Release 5, 4, 4.5, 3, 2 or 1 for only $495.00 academic, $860.00 commercial! Contact sales@hyper.com or one of our Authorized Dealers today! 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 7.01 communicate! Update to Release 7.01

11. Form For PDB Query Search engine for visualizing 3D biomolecular models. http://molbio.info.nih.gov/cgi-bin/pdb

Welcome to the NIH Molecules R US Utililty . This facility combines a full text search of the PDB database with a FORM interface to customize the format ( TEXT, IMAGE, INTERACTIVE ) of the selected structure. Please read the instructions! Initiate a PDB query. What's NEW

12. Introduction To Molecular Modeling Read an indepth introduction to molecular modelling with diagrams, equations, and notes. What is molecular modeling? molecular modeling, also known as molecular mechanics, is a method to calculate the http://chemistry.gsu.edu/glactone/modeling/MMintro.html

What is Molecular Modeling? In a very crude sense molecular modeling treats a molecule as a collection of wieghts connected with springs, where the weights represent the nuclei and the springs represent the bonds. A force field is used to calculate the energy and geometry of a molecule. It is a collection of atom types (to define the atoms in a molecule), parameters (for bond lengths, bond angles, etc.) and equations (to calculate the energy of a molecule). In a force field a given element may have several atom types. For example, ethylbenzene contains both sp -hybridized carbons and aromatic carbons. sp -Hybridized carbons have a tetrahedral bonding geomtery, while aromatic carbons have a trigonal bonding geometry. The C-C bond in the ethyl group differs from a C-C bond in the phenyl ring, and the C-C bond between the phenyl ring and the ethyl group differs from all other C-C bonds in ethylbenzene. The force field contains parameters for these different types of bonds. Some of these parameters are given below. The total energy of a molecule is divided into several parts called force potentials, or potential energy equations. Force potentials are calculated independently, and summed to give the total energy of the molecule. Examples of force potentials are the equations for the energies associated with bond stretching, bond bending, torsional strain and van der Waals interactions. These equations define the potential energy surface of a molecule. E TOTAL = E STRETCH + E BEND + E S-B + E

13. CAChe Group/Fujitsu | Chemistry Products Experimental chemists use CAChe to view and predict 3D molecular structure, to predict properties and to analyze the relationship between structure and properties or structure and reactivity. CAChe is a tool for medicinal, polymer, process and synthetic chemists. http://www.cachesoftware.com/

CAChe Group is a leading provider of computer-aided chemistry software and services for predicting molecular structure, properties, spectra, reactions, thermodynamics, and kinetics. What's new APPLY NOW! Sales Director for CAChe based in Portland, Oregon Technical Field Sales Specialist for CAChe based in Portland, Oregon PRODUCTS CAChe 5 -New Release BioMedCAChe -New Release Materials Explorer 2.0 -New Release MOPAC 2002 -4x more accurate calculations! Teaching with CAChe instructor workbook -Download now! NEWS CAChe 5.04 and BioMedCAChe 5.04 released October 14, 2002. Click here for more information. RW Johnson's Director of Computer-Aided Drug Discovery discusses the need for chemistry software­-CAChe-­for every experimentalist, World Pharmaceutical Development Learn more about predicting environmental remediation rates with CAChe, Today's Chemist at Work CAChe receives one of "Top 5 Chemistry Products Awards," based on products that generated the most reader response over a 12 month period. CAChe receives "Reader's Choice Award Finalist," reflecting the products readers found exceptional based on value, reliability, quality, and ease of use.

14. TINKER Molecular Modeling Package A free molecular modeling package for molecular mechanics and dynamics, with some special features Category Science Chemistry Software Biomolecular...... The TINKER molecular modeling software is a complete and general package for molecularmechanics 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 3.9 Major Release Date: June 2001 Last Minor Revision: December 20, 2001 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 and ff96, CHARMM 19 and 27, MM2(1991), MM3(2000), OPLS-UA and OPLS-AA. 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 curent release, version 3.9 contains the following new features and updates from version 3.8: (1) improved nucleic acid building from sequence and automated conversion of nucleic acid PDB files to and from the TINKER format, (2) a new rigid body dynamics facility, (3) ability to handle infinite polymer lattices such as diamond and graphite, (4) treatment of intramolecular polarization via the Thole method, (5) a new utility program to compute molecular polarization, (6) an improved RasMol-based viewer that accepts TINKER coordinate files, allows atom selection, etc., (6) an optional Andersen stochastic collision thermostat for MD, (7) where appropriate TINKER programs such as ANALYZE, SUPERPOSE and SPACEFILL accept multiple coordinate set "archive" files as input, (8) updated parameter sets for various of the supported force fields.

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

16. 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.

17. Springer LINK: Journal Of Molecular Modeling The Journal of molecular modeling is the perfect medium for publishing of researchresults produced by frequent and sophisticated use of computational methods http://link.springer.de/link/service/journals/00894/

Editor-in-Chief: Tim Clark Would you like to automatically receive every new table of contents of Journal of Molecular Modeling ? Then register with our free-of-charge mail service LINK Alert by checking the appropriate box(es) and enter your email address here: Online First Articles only Printed issues only You will receive confirmation via email. ISSN: 0948-5023

18. 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/

19. Molecular Modeling Heidelberg Category Science Chemistry Computational 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+

20. Molecular Modelling Group One of the Specialist Interest Groups of the Royal Society of Chemistry. Links to research groups, meeting reports, software archives, selected articles. http://www.rsc.org/lap/rsccom/dab/ind006.htm

Molecular Modelling Group Mission Statement "To stimulate the use and application of molecular modelling and related methods in Industry" Aims To raise awareness of molecular modelling To promote the cost-effectiveness of molecular modelling and related methods in experimental programs of research across all industrial sectors To facilitate the use of molecular modelling and related methods by Small and Medium Enterprises (SMEs) across the UK by arranging seminars and meetings for research managers and technical personnel To identify expertise in problem solving and the provision of appropriate molecular modelling solutions for industrial research applications To inform members of advances in the applications and development of molecular modelling and to update members on the performance of hardware and software To promote the synergistic interaction of this Specialist Interest Group with others, both within the RSC and outside, in industry and academia, in the UK and abroad To influence and advise government departments and agencies Forthcoming Events Click here to search the chemsoc Conferences and Events database for meetings organised by the Molecular Modelling Group Submit details of a Group meeting to the chemsoc Conferences and Events database Annual Events Cutting Edge Approaches to Drug Design A series of annual one day meetings addressing the role of state-of-the-art informatic technologies in drug design

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