1. Protege-2000 Class Molecular_Modeling Documentation Project nciOncology Class molecular_modeling. Concrete Class Extends Computer_Modeling Direct Instances None Direct Subclasses Homology_Modeling http://www.mindswap.org/2003/CancerOntology/htmls/Molecular_Modeling.html

Project: nciOncology Class Molecular_Modeling Concrete Class Extends Direct Instances: None Direct Subclasses: Template Slots Slot name Documentation Type Allowed Values/Classes Cardinality Default Instance Instance Instance Instance Instance Instance Instance Instance Instance Instance Instance Own Slots Slot name Documentation Type Value Cardinality Instance Return to class hierarchy Generated on Fri Aug 01 19:28:21 EDT 2003

2. Bioinformatik.de - /Software/Unix/Molecular_Modeling/ bioinformatik.de /Software/Unix/molecular_modeling/ http://www.bioinformatik.de/cgi-bin/browse/Catalog/Software/Unix/Molecular_Model

Match: All Any Boolean Category bioinformatik.de Software Unix Molecular Modeling BRAGI is a interactive protein-modelling program. It was developed for the special purpose to modell unknown proteins from the structure of a known one. http://www.uni-koeln.de/math-nat-fak/biochemie/ds/dsbrag_e.htm DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. http://dirac.cnrs-orleans.fr/DomainFinder/ GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. http://igc.ethz.ch/gromos/ Mc-Sym (Macromolecular Conformations by SYMbolic programming) is the result of a joint effort between the computer science and biochemistry departments of the Université de Montréal to develop a tool for three-dimentional determination of RNA structures. http://www-lbit.iro.umontreal.ca/mcsym/ Molecular Simulations Inc. (MSI)- is a leading provider of molecular modeling and simulation software for both life and materials science research. http://www.msi.com/

3. 101.11.13 0911 BE\htdocs\molecular_modeling 101.11.13 0911 BE\htdocs\molecular_modeling\computational_methods.html bohr_root /var/www/htdocs/molecular_modeling computational_methods.html http://bohr.winthrop.edu/molecular_modeling/WS_FTP.LOG

4. Defintion Of Molecular_modeling - Chemistry Dictionary Chemistry definition and meaning of molecular_modeling. molecular_modeling explained by Chemicool. http://www.chemicool.com/definition/molecular_modeling.html

Periodic Table Forum Chemistry Dictionary Chemistry Tools ... Link to Us Search by name or symbol: Definition of Molecular modeling Molecular modeling is a technique for the investigation of molecular structures and properties using computational chemistry and graphical visualization techniques in order to provide a plausible three-dimensional representation under a given set of circumstances. About Contact Privacy Biology ... Equations

5. Science, Biology, Bioinformatics, Molecular Modeling - Canadaspace.com Canadaspace.com. Canadian Search Engine. Science, Biology, Bioinformatics, Molecular Modeling. http://www.canadaspace.com/CS/Science/Biology/Bioinformatics/Molecular_Modeling

Home Local News Directory ... Resources Search for: in: Canadian Sites All The Internet Images Google Yahoo Altavista Fast Ask Jeeves Lycos MSN Wisenut Hotbot AOL Search Teoma Search Resources Canada Local Search Canadian News Canadian Web Directory Top Canadian Websites ... Canadian Web Resources Molecular Modeling Home Science Biology Bioinformatics ... partner with us

6. Molecular Modeling Course 2007 General program. I. Database Tools/Informatics II. Macromolecular Tools/Databases III. Molecular Modeling Techniques large molecules http://www.oci.unizh.ch/diversa/Molecular_Modeling/

Home Program-Tutors Application Location ... Contact off-semester courses Institute of Organic Chemistry About the Event canceled General program: I. Database Tools/Informatics II. Macromolecular Tools/Databases III. Molecular Modeling Techniques - large molecules IV Molecular Modeling Techniques - small molecules V. QSAR and Docking VI. Exam/General Course Assessment People Engelbert Zass, ETH Bernd Schweizer, ETH Katja Zerbe, UZH Kerstin Möhle, UZH ... Kim Baldridge, UZH Related Links University of Zurich Institute of Organic Chemistry Contact @webmaster Institute of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland XHTML CSS Web site Design by : WDD

7. Molecular_Modeling.html Intro to Molecular Modeling. Molecular modeling has advanced rapidly during the past decade because of amazing advances in software and hardware. http://k2.chem.uh.edu/Chem3111/Molecular_Modeling.html

HTML> Intro to Molecular Modeling Molecular modeling has advanced rapidly during the past decade because of amazing advances in software and hardware. We will be using this in the lecture and laboratory this semester. Beyond simple visualization is an much complex (i.e. expensive) type of program that allows you to build structures with a graphical user interface (GUI), perform various levels of computational modeling and visualize the results. Notwithstanding their sophistication, the best of these programs still are remarkably easy to use. Three basic "models" exist. In order of increasing sophistication (and demands for computer resources), these models are: Force Field or "Molecular Mechanics" : Molecules are treated primarily by classical mechanics as balls held together by springs. Stretching, bending, twisting and coulombic interactions are all described by Hooke's law potentials and force constants that are often derived from experiment. Calculations are fast even for large molecules. Semiempirical Methods Ab Initio ("from basic principles") methods

8. Discover Life from the Open Directory Project and is subject to their licence. Click on blue links (++ open; close). Return to Find. Browsing molecular_modeling http://pick4.pick.uga.edu/mp/20n?act=get_value&db=NAME&key=Molecular_Modeling&sl

9. Analysis & Visualisation Of Electric Fields & Charges In Mathematica The University of Queensland VisLab Analysis Visualisation of Electric Fields Charges in Mathematica. http://www.vislab.uq.edu.au/research/molecular_modeling/index.html

All UQ IN THIS SECTION QUICK LINKS About Us Education User's Info Sitemap ... Print version Analysis and Visualisation of Electric Fields and Charges in Mathematica Tyrone Curtis - Honours student, School of Physical Sciences, University of Queensland This page represents a summary of the work completed by Tyrone Curtis and Edan Scriven as research assistants for Professor Bernard Pailthorpe over Summer 2005/2006. These files were written to visualize molecules using data generated by the Molecular Dynamics program Gromacs and because there weren't many programs like this already in existence. It is hoped that these notebooks will aid in the understanding of the electrical properties of systems being studied. All Mathematica files were generated using Mathematica 5.1. As such, there may be incompatibilities with earlier versions of Mathematica. The files located on the following pages are free to download and use. 2D Visualization of Electric Fields and Electric Potential of Point Charges A Mathematica notebook for generating equipotentials and field lines for point charges in a 2D plane. Also features a Mathematica package for labelling contour plots. 2D Visualization of Electric Fields of Point Charges around a Dielectric Interface Includes a Mathematica notebook for plotting equipotentials and field lines for point charges on either side of an interface between media of different dielectric constants.

10. Molecular Modeling - Labwebwiki days/ns WallClock 493.837555 Efficiency 100% 8 CPUs and more FAILS. Retrieved from http//139.57.180.167/wiki/index.php/molecular_modeling http://139.57.180.167/wiki/index.php/Molecular_modeling

Molecular modeling From Labwebwiki Jump to: navigation search Contents Introduction His-tagged PSII Point Mutants PSII core simulation system, built using 1S5L structure file Miscellanious software installed on our workstations ... edit Introduction Molecular dynamic simulations provide information concerning the thermal movements of proteins and chromophores. They offer molecular trajectories of motion that have the potential to far surpass the amount of information contained in static X-ray structures.We are working on application of MD simulations to the PSII core complex in its native membrane environment. Snapshot of PSII core complex simulation system. A -top view, B - view from the side of the membrane We use the time-dependent structures as the basis for kinetic models of excited state dynamics to see how protein dynamics affects the efficiency of energy transfer within PSII. We have calculated excited state properties of individual chromophores ab initio , based on the nuclear configurations emerging from the molecular trajectories of motion. This allowed us to determine the site energy or colour of each chromophore in PSII as well as how that colour changes in time. Slow nuclear modes cause fluctuations of S1 excited states Currently we are trying to understand how relaxation of the protein in responce of the photochemical charge separation helps to make this reaction in biological photosystems virtually irreversible.

11. Molecular Modeling Software CD Bank cataloguer 2.7.5 CD Bank will help you maintain and organize a catalog of your media collection, including CDROMs, audio CDs, DVDs or any other http://www.allworldsoft.com/keywords/molecular_modeling/

PDF to Word Converter (PDF2Word) 1.6 Super Bubbles 1.30 Over 150 hand-crafted levels of bubble moving action really make this one unique. The challenge stage could be a whole game on its own! Freeware Shareware Demo Commercial Example: KaZaA New TOP Most popular ... Home Molecular modeling software Related keywords: Modeling Modeling Tool modeling Analog Modeling ... Web Development Number of references on page: Language: Any English German French Italian ... Spanish License: Any Freeware Shareware Demo Adware ... Data Only Installation: Any Install and Uninstall Install Only No Install Support Uninstall Only Operational system: Any Windows 95 ME NT XP ... Mac No pages were found. Make sure all words are spelled correctly. Try different keywords. Try more general keywords. Related information More free downloads to consider Dynasite 2.0 Cryptomathic File2File 2.0 NeoLite 2.0 MMD CamExplorer Free 3.1 ... SQL Designer 1.3 More search terms dbx with vb.net irfanview fax checkers mcp exam 70-029 ... Home Molecular modeling software AnyBook Pro II - Publishers Business Kit 9.41 SmartFormFiller 5.1 CD Bank cataloguer 2.7.5 Contact Page

12. Research Compendium: Biotechnology, Bioengineering And Biomedical Applications - Search Table of Contents. List of Researchers using molecular_modeling methodology. Displaying Researchers 1 thru 2. Found 2 Researchers out of 298 in the http://gsapply.uml.edu/biocompen/method/tableviewP.lasso?-database=bioCompen.FP3

13. Molecular Modeling - Wiktionary originally involved the building of physical models, but now uses computer simulation. Retrieved from http//en.wiktionary.org/wiki/molecular_modeling http://en.wiktionary.org/wiki/molecular_modeling

molecular modeling From Wiktionary Jump to: navigation search edit English edit Noun Wikipedia has an article on: Molecular modeling Wikipedia molecular modeling chemistry a number of techniques for studying molecules and their interaction ; originally involved the building of physical models , but now uses computer simulation Retrieved from " http://en.wiktionary.org/wiki/molecular_modeling Category Chemistry Views Entry Discussion Edit History Personal tools Log in / create account Navigation Main Page Community portal Requested entries Recent changes ... Contact us Search Toolbox What links here Related changes Upload file Special pages ... Permanent link This page was last modified 21:22, 12 September 2007. Content is available under GNU Free Documentation License About Wiktionary

14. [gmx-users] Re: Mdrun -rerun And Box Size Bug Not Fixed? D Molecular Modeling Group Swiss Institute of Bioinformatics CH1015 Lausanne, Switzerland www.isb-sib.ch/groups/molecular_modeling.htm http://www.gromacs.org/pipermail/gmx-users/2007-November/030614.html

[gmx-users] Re: mdrun -rerun and box size bug not fixed? Michel Cuendet michel.cuendet at isb-sib.ch Wed Nov 7 18:13:00 CET 2007 Previous message: [gmx-users] installation error Next message: [gmx-users] Re: mdrun -rerun and box size bug not fixed? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] version of gmx, platform, huge compressibility, turning off the michel.cuendet at isb-sib.ch gmx-users at gromacs.org 20071102152757.0FAFD2435D at xray.bmc.uu.se > Hi, I think I got it :-) Using gmx 3.3.1 with the same thermostat and barostat settings as the original run, I get the right LJ energies within 0.1%. I used tcoupl and pcoupl = "no" because I somehow remembered that thermostats could do weird things when rerunning (see the old thread : http://www.gromacs.org/pipermail/gmx-developers/2005-August/001290.html ) But apparently the box is not reread form the trajectory if the pcoupl option is deactivated. It would be much safer for users if the appropriate options were automatically set when -rerun in invoked: nstlist = 1 nstenergy = 1 NO rescaling of velocities NO rescaling of box size Do read the box sizes from the trajectory Cheers, Michel ========================================================== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm ========================================================== ========================================================== Michel Cuendet, Ph.D Molecular Modeling Group Swiss Institute of Bioinformatics CH-1015 Lausanne, Switzerland www.isb-sib.ch/groups/Molecular_Modeling.htm ==========================================================

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17. Information For New Users Of The Molecular Modeling Facility 1102 Natural Sciences 2 University of California, Irvine, California, 926972025 phone (949) 824-4097 fax (949) 824-8571 http://www.chem.uci.edu/research/facilities/molecular_modeling/newuser.shtml

Home Home Welcome Welcome Faculty Faculty Staff Staff Research Research Centers Centers Facilities Facilities Graduate Graduate Undergraduate Undergraduate Alumni Alumni Courses Courses Seminars Seminars Outreach Outreach Employment Employment 1102 Natural Sciences 2 University of California, Irvine, California, 92697-2025 :: phone (949) 824-4097 :: fax (949) 824-8571 Information for New Users of Molecular Modeling Facility Please change the password using the command 'passwd' when you log in the first time. Your account is good on the following machines in Rowland room 517: model1 through model6. You can log in remotely using F-Secure ssh to: modelx.ps.uci.edu where x is a number 1-6. If you want to get an orientation to the Facility or any of the software, please contact me. I am available to help make the Facility work for you. If you have any questions or problems, please contact me at X 1204 or e-mail to model@uci.edu

18. Molecular Modeling - The Cluster Agenda Retrieved from http//agenda.clustermonkey.net/index.php/molecular_modeling . This page has been accessed 559 times. This page was last modified 1410, http://agenda.clustermonkey.net/index.php?title=Molecular_Modeling&printable=yes

19. Molecular Modeling - Health Encyclopedia Retrieved from http//www.steadyhealth.com/encyclopedia/molecular_modeling . Would you like to discuss or post question about Molecular modeling ? http://www.steadyhealth.com/encyclopedia/Molecular_modeling

var skin = 'monobook';var stylepath = '/encyclopedia/skins'; Molecular modeling From Health Encyclopedia Jump to: navigation search edit See chemical model computer simulation molecular dynamics edit Facts (generated by robot; please edit if you find it inaccurate) The Journal of Molecular Modeling is the first journal in chemistry to offer network, print based and CD-ROM editions. NIH Guide to Molecular Modeling is a site with some important links at the National Institute of Health (NIH) (Updated 4/12/99). Molecular Modeling The term molecular modeling is used to describe the study of molecules and molecular systems by means of computer models. Licenses for PC Fifteen Pentium II Lab Workstations Using the SGI modeling lab Information on Molecular Modeling Molecular Modeling is the 3 dimensional rendering of molecules in an environment produced by computer graphics. Retrieved from " http://www.steadyhealth.com/encyclopedia/Molecular_modeling Would you like to discuss or post question about Molecular modeling Click here !

20. Tiscali - Search molecular_modeling .Biomolecules. Sites seleccionados desde la categoría Biomolecules. 1.AMMP. A free program suite for molecular mechanics, dynamics and http://directory.tiscali.es/Science/Chemistry/Molecular_Modeling/Biomolecules

.home search directorios Science ... Chemistry  .Biomolecules Sites seleccionados desde la categor­a Biomolecules AMMP A free program suite for molecular mechanics, dynamics and modeling with some special features like docking or ab initio DFT calculations. Runs under Linux/Unix and Win9x. The site provides access to the documentation and offers on-line tutorials. Amber A general purpose molecular mechanics and molecular dynamics package with the capability to compute free-energy changes. B: On-line Molecular Modeling "B" (formerly known as Biomer) is a java-based 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. Biomolecular Modeling Information Server Web resources including: theory and methods of computational modeling, alphabetical software and database directory. Bionet.software.x-plor Archive of newsgroup for X-PLOR software for 3D macromolecular structure determination. CHARMM A program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images.

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