21. Molecular Modeling Center Details research initiatives, with project backgrounds, descriptions, facilities and resource utilization, along with HyperChem software documentation. http://molmod2.chem.georgetown.edu/

Welcome to Georgetown Molecular Modeling Center Home Page ! Recent Announcements for MMC Group (last updated October 9, 2002) Backgound of Molecular Modeling Frequently Asked Questions (FAQ) of Molecular Modeling. Gallery A HyperChem Quick Start Computing Facilities Useful FREE software on the Web Other Molecular Modeling Groups on the Web Other links Older Announcements for MMC Group Older Project description and research activities list Maintained by Arnie Miles email : adm35@georgetown.edu Advanced Research Computing Georgetown University on behalf of the Georgetown University Chemistry Department last updated 10/10/2002 11:07 AM "This material is based upon work supported by the National Science Foundation under Grant No. CHE-9601976." "Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation." Powered by

22. The Babel Home Page A program designed to interconvert a number of file formats currently used in molecular modeling. http://smog.com/chem/babel/

Babel - A Molecular Structure Information Interchange Hub by Pat Walters and Matt Stahl Research Advisor Prof. Dan Dolata Artificial Intelligence in Chemistry Lab Department of Chemistry University of Arizona Tucson, AZ 85721 babel@mercury.aichem.arizona.edu Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0. Babel is capable of assigning hybridization, bond order, and connectivity when these elements are not present in the input file. Supported Input Formats Supported Output Formats View the README file Download A Copy of Babel ... Register your copy of Babel Babel was designed so that new file formats could be easily added by the end user. The addition of a file format to Babel typically consists of merely creating the "reader" and/or "writer" routines and adding a few lines of code to the main program. For those interested in adding new file formats we have produced The Babel Developer's Guide

23. NCBI Structure - MMDB Page NCBI's structure database is called MMDB (molecular modeling DataBase), and it isa subset of threedimensional structures obtained from the Protein Data Bank ( http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml

PubMed BLAST OMIM Taxonomy ... Entrez Structure Search Entrez PubMed Protein Nucleotide Structure Conserved Domains 3D-Domains Genome PopSet Taxonomy OMIM for MMDB Help Short summary MMDB Help Detailed explanations Linking to MMDB direct WWW access to the MMDB server Read about MMDB Papers about MMDB PDBeast Taxonomy in MMDB 3D-structure viewer CDD Conserved Domain Database VAST Structure comparisons VAST Search Submit structure database searches Research Research topics and staff MMDB - Entrez's Structure Database NCBI's Entrez includes a database of experimentally determined three-dimensional biomolecular structures. Most 3D-structure data are obtained from X-ray crystallography and NMR-spectroscopy; they provide a wealth of information on the biological function, on mechanisms linked to the function, and on the evolutionary history of and relationships between macromolecules. Our goals in adding structure data to Entrez are to make this information easily accessible to biologists, and to facilitate comparative analysis involving 3-D structure. NCBI's structure database is called MMDB (Molecular Modeling DataBase), and it is a subset of three-dimensional structures obtained from the Protein Data Bank (

24. Center For Molecular Modeling http://cmm.cit.nih.gov/modeling/

25. 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, "

26. MATHMOL MODULES Concepts in Science through molecular modeling. Activities for Students and Teachers. Moleculesof 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

27. CMS Molecular Biology Resource Excellent compendium of Internetaccessible analytical tools and resources for Molecular Biology, Biotechnology, Molecular Evolution, Biochemistry, and Biomolecular modeling from the UCSD Supercomputer Center. http://www.sdsc.edu/ResTools/

Sequence Databases Physico-Chemical Features Analyses Enzyme Info and Structure Databases Organism-Specific Genome Databases ... Make a URL Contribution Version 6.3.5, March 2002

28. Molecular Modeling Home Page Frames version molecular modeling for Chemical Education. us feedback. ASlide Show describes uses for molecular modeling. Top 5% chemistry 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.

29. K-12 Activities MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for K12 students and teachers interested in the field of molecular modeling and its application to mathematics. http://www.nyu.edu/pages/mathmol/K_12.html

MathMol K-12 Activity Page MathMol (Mathematics and Molecules) is designed to serve as an introductory starting point for K-12 students and teachers interested in the field of molecular modeling and its application to mathematics. MathMol Quick Tour: What is molecular modeling? Why is it so important? What is the relationship between molecules and mathematics? Hypermedia Textbook for Grades 6-12 Library of 3-D Geometric Structures The MathMol Library of Geometric Structures contains GIF and and 3-D (VRML) files of geometric structures that are found in most intermediate school textbooks. Hypermedia textbook for Elementary School A textbook designed especially for students in grades 3-5. 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. Water Module for K-12 Students Learn about water. Calculate the density for water and ice using on-line interactive activities. Concept in Science through Molecular Modeling Contains information and interactive activities for students and teachers.

30. Gilson Group Home Page Research information and training opportunities in molecular modeling, computational chemistry, and chemoinformatics. http://gilsonlab.umbi.umd.edu

Gilson Laboratory Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute Group Members Rsrch Environmnt Graduate Studies Postdoc Studies ... Giving a seminar Last modified: Thursday, 14-Nov-2002 12:52:24 EST

31. Molecular Modeling Of Proteins molecular modeling of Proteins. Journal of Molecular Biology. Journal of MolecularModeling (the first fully electronic journal in chemistry). Protein Science. http://solon.cma.univie.ac.at/~neum/protein.html

Molecular Modeling of Proteins ``It is God's privilege to conceal things, but the kings' pride is to research them.'' (Proverbs 25:2; ascribed to King Solomon of Israel, ca. 1000 B.C.) The protein folding problem entails the mathematical prediction of (tertiary, 3-dimensional) protein structure given the (primary, linear) structure defined by the sequence of amino acids of the protein. It is one of the most challenging problems in current biochemistry, and is a very rich source of interesting problems in mathematical modeling and numerical analysis, requiring an interplay of techniques in eigenvalue calculations, stiff differential equations, stochastic differential equations, local and global optimization, nonlinear least squares, multidimensional approximation of functions, design of experiment, and statistical classification of data. Even topological concepts like the Morse index and invariants in knot theory (Jones polynomials) have been discussed in this context. An extensive recent report from the U.S. National Research Council

32. Computational Chemistry And Molecular Modeling Service for chemical pictures, animations, 3D files and molecular properties (HOMO, LUMO, charges, dipole, spin). http://www.molecular-modelling-service.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

33. ECHET96: Molecular Modeling And Databases molecular modeling and Databases. Text Keynote, Stereocontrolled Reactions,New Synthetic Methodology, Reaction Mechanisms and Conformational http://www.ch.ic.ac.uk/ectoc/echet96/modelling_ga.html

Molecular Modeling and Databases Text: Keynote Stereocontrolled Reactions New Synthetic Methodology Reaction Mechanisms and Conformational Analysis and Molecular Modeling and Databases Graphical Abstracts: Keynote Stereocontrolled Reactions New Synthetic Methodology Reaction Mechanisms and Conformational Analysis and Molecular Modeling and Databases Text: Keynote Stereocontrolled Reactions New Synthetic Methodology Reaction Mechanisms and Conformational Analysis and Molecular Modeling and Databases Graphical Abstracts: Keynote Stereocontrolled Reactions New Synthetic Methodology Reaction Mechanisms and Conformational Analysis and Molecular Modeling and Databases

34. Molecular Modeling molecular modeling. Protein Modeling. PDB The Protein Data Bank, ishosted by the Research Collaboratory for Structural Bionformatics http://amanda.uams.edu/mm.html

Molecular Modeling Protein Modeling PDB The Protein Data Bank, is hosted by the Research Collaboratory for Structural Bionformatics use this resource for the latest crystal structures of proteins, nucleic acids and carbohydrates. QSAR Quantum Mechanics Example Molecules Links to related topics Send the BVC your Questions/Comments Underlined Topics are HotLinks Note: More to come.

35. 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

36. Fred K. Friedman, Ph.D. Structure, function, mechanism and regulation of the drug and carcinogen metabolizing cytochrome P450 enzymes are studied by biochemical, biophysical and enzymology approaches, and by molecular modeling. http://rex.nci.nih.gov/RESEARCH/basic/lm/fkf.htm

Center for Cancer Research National Cancer Institute National Institutes of Health The web address for Dr. Fred K. Friedman's home page has changed. Please click here for the new address and update your bookmarks. Last revised on September 18, 2002 by Linda Byrd Return to Laboratory of Metabolism

37. 3D Molecular Modeling Homepage Of Tokyo University Of Pharmacy Presently our research work is focused on the molecular modeling of pharmaceuticalstructures through computational chemistry, and the recognition of molecular http://triton.ps.toyaku.ac.jp/~dobashi/english/

38. BioNavigator | Your Log-in Page eBioinformatics offers BioNavigator a webbased service incorporating tools and databases from many sources; enabling you to perform sequence analysis, database searching, PCR primer design, and molecular modeling. http://www.BioNavigator.com/

39. Home A free molecular modeling program for Windows9x operating systems with 3Dbuilder, various ab initio calculation modules and simple molecular mechanics. http://www.planaria-software.com/

We sell the popular ArgusLab molecular modeling program. Used by thousands in industry and education around the world. Download the full-featured trial version now Visit our webstore Only $25 for a 1-year academic license New Version 3.1 With an Improved Builder and Presentation Graphics ArgusLab 3.1 Now exports to POV-Ray image files! (click small picture for larger view) Contact Information Planaria Software PO Box 55207 Seattle, WA 98155 FAX: 206-440-3305 General Information: info@planaria-software.com Sales: sales@planaria-software.com

40. UWMML At Pharmacy Click here Tripos/Sybyl course announcement. Sybyl molecular modeling softwareis available as a seat on the University of Wisconsin site license. http://uwmml.pharmacy.wisc.edu/

UWMML Web Page University of Wisconsin Molecular Modelling Laboratory, Rm. 7205 School of Pharmacy, 777 Highland Ave., Madison, Wisconsin 53705-2222 Professor Dan Rich dhrich@facstaff.wisc.edu Associate Scientist Ken Satyshur satyshur@wisc.edu 608-262-9403. Or contact me on my cell phone: 608-215-5207, Which also takes e-mail: 6082155207@vtext.com Serving the Pharmacy community since 20/Sep/1994:13:32:29. Last modified Nov 3, 2002 OUR EIGHTH ANNIVERSARY!! This is a composite stereo picture. This is the CORRECT kind of stereo image to publish in a journal. If you see crossed stereo, view the middle and right images. If you see relaxed stereo, view the left and middle images. If you don't know which method you use to see stereo, view the images and note if the phenyl under the yellow dots comes toward you or away from you. Find out the answer by clicking here!! How to See Stereo Modelling Pictures! Sybyl Modeling Web Page Click here: Tripos/Sybyl course announcement. Sybyl molecular modeling software is available as a seat on the University of Wisconsin site license. Sybyl, by Tripos Corp (www.tripos.com), is a full featured modeling package that is used to create, manipulate, and display molecules and polymers. It is especially suited to biological compounds with the "biopolymer" module. Proteins, DNA, and RNA can be displayed andmanipulated in various formats, including sticks, surfaces and ribbons. High quality images can be saved in various formats for publication in print, as html, or for input to powerpoint. There are 14 seats now in use for students and faculty. The site is sponsored by the Chemistry department (prof. Dan Rich) and is served by Melissa Lucero (lucero@chem.wisc.edu) and Ken Satyshur (satyshur@uwmml.pharmacy.wisc.edu). Please contact them if you wish to join the site license.Things to do at this site:

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