61. Molecular Modeling Laboratory-Home Page Includes information on the software used, one course that uses the laboratory, and links to the personal pages of lab personnel. http://cesario.rutgers.edu

Structural Biology Computational Laboratory at Cook College of Rutgers University Located in: Room 202, Lipman Hall Home of the Department of Biochemistry and Microbiology 76 Lipman Drive, New Brunswick, New Jersey 08901 The molecular modeling laboratory provides students, staff, and faculty the ability to build and graphically manipulate 3-D images of complex molecules such as proteins and nucleic acids using Insight II software developed by Molecular Simulations (now Accelrys ). The premium modules perform complex molecular and quantum mechanical calculation and protein structure homology analysis. Files in standard formats such as that of the Protein Data Bank can be imported. Use the SOFTWARE link for an extensive listing of available software Use the HELP! link for laboratory help files. Use the Homology Modeling Class link for the class homepage. Use the General Biochemistry link for annotated links related to Biochemistry Staffed Hours: M-F 9am-5pm Use during unstaffed hours by arrangement Questions can be sent to Rob Muldowney Development of the laboratory was done by E. Allen Smith

62. CCL Home A resource for computational chemists. Discussions on chemistry software, data, conferences, jobs, quantum chemistry, molecular mechanics, molecular dynamics, QSAR, molecular graphics, molecular modeling, and associated archives http://www.ccl.net/chemistry/

Page supported by: http://www.ccl.net/chemistry/index.shtml CCL Home About CCL Rules Instructions Contributing Material ... Send E-mail to CCL Administrators Welcome to the CCL Website! Thank you CCL Supporters How can you support CCL CCL is now located at the Science Computing Facility at the College of Science of the University of Notre Dame in Indiana. If you have problems sending mail to the list, please contact the list administrator directly at and send a copy of your message. It will be eventually resent. Since we are getting a lot of spam mail, we had to blacklist many addresses which originate spam. You can check blacklisted subnets at http://www.ccl.net/spammers.txt (watch, it is several Megabytes). We do admit (and apologize) that most of these addresses are the victims of crackers who used machines in the ajacent subnet to send spam. Even if your address is on the list, you are probably a victim as we all are. The list is ordered by IP address. Please tell us if your address is there, and we will promptly remove it. Note, if you are using some popular mail service, which was compromized by the bad guys at some point, it may be blacklisted, and your messages to CCL may be rejected. Let us know about it (at ) and we will remove your address from the blacklist.

63. SIMION 3D 7.0 - The Ion And Electron Optics Simulator SIMION ion optics software and more than 200 scientific software products in mass spectrometry, chromatography, quality control, chemical inventory, MSDS, molecular modeling, database, and plotting. Online ordering. http://www.sisweb.com/simion.htm

Scientific Instrument Services, Inc. Supplies and Services for Mass Spectrometers, Gas Chromatographs and Liquid Chromatographs Search: Home Products Services Catalog ... Employment SIMION SIMION Overview Brochure (PDF) SL Toolkit (NEW) SIMION.com Ordering SIMION The Industry Standard for Ion Optics Simulations www.SIMION.com We invite you to visit our new www.simion.com web site, which contains many more resources and hosts the SIMION Users Group for discussions between SIMION users. Windows Version Click here to download latest SIMION 7.0 Demo. The software is widely used by manufacturers and designers of mass spectrometers, electron microscopes, electron multipliers and other scientific instruments. Using this software, instrument designs have been perfected and the sensitivities of the instruments have been maximized. Here at Scientific Instrument Services we have been using this software to study mass spectrometer sources and filaments. Using this system we have been able to study the filament shape, the effect of filament shields and the effect of the filament magnet. This information is being used to design new filaments and other mass spec accessories which will be added to our product lines in the future. The original version of SIMION was an electrostatic lens analysis and design program developed by D. C. McGilvery at Latrobe University Bundoora Victoria, Australia, 1977. SIMION for the PC was developed at the Idaho National Engineering Laboratory. SIMION 7.0 is a completely new version which contains major improvements over the previous six versions. User programs have been greatly expanded and are more powerful. A new geometry file option supports highly complex array geometry. Extensive algorithm modifications have greatly improved the computational speed and accuracy. This C based program can model complex problems using an ion optics workbench that can hold up to 200 2-D and/or 3-D electrostatic or magnetic field arrays. These arrays can have up to 50,000,000 points which can be visualized as 3D objects that the user can cut away to inspect ion trajectories and potential energy surfaces.

64. Molecular Modelling Toolkit MMTK is based on an objectoriented model of molecular systems. It emphasizes Python programming aspects rather than molecular modeling. http://starship.python.net/crew/hinsen/mmtk.html

The Molecular Modelling Toolkit European mirror This page describes an older version of MMTK which is still available for compatibility reasons. See the new MMTK home page for the current version. The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. MMTK program in a PTUI window using VMD for visualization This software is MMTK is developed in and around Python , a high-level object-oriented general-purpose programming language. In fact, MMTK consists of nothing more than a collection of Python modules, most of which written in Python itself, with only a small time-critical part (e.g. energy evaluation) written in C. MMTK applications are Python programs that make use of these modules. Python was chosen because it allows rapid code development and testing, while providing a very convenient C interface for dealing with time-critical calculations. MMTK is based on an object-oriented model of molecular systems. A system is made up of molecules, complexes, and atoms, all of which are defined in a central database of definition files, which themselves are (very simple) Python programs. A molecule, for example, is defined in terms of atoms, functional groups, bonds, force field parameters etc. It is possible to introduce specialized versions of these objects; for example, MMTK has special support for proteins, which are basically chemical complexes, but can be handled in terms of peptide chains, residues, sidechains etc.

65. Jerome Baudry's Page. Molecular Modeling, Drug Design Applications of molecular modeling and computational chemistry to biophysics of large, integrated biosystems. http://www.ks.uiuc.edu/~jerome/

Jerome Baudry Our research IN THE NEWS Present position: Senior Research Scientist School of Chemical Sciences Computer Applications and Network Services Noyes Lab, Room 150 University of Illinois at Urbana-Champaign e-mail : jerome@scs.uiuc.edu See Resume (updated May 2004) E-mail at Beckman: jerome@ks.uiuc.edu Education: December 1997 : Ph.D., Molecular Biophysics (Tres Honorable avec Felicitations du Jury - summa cum laude). Title : Theoretical study of H-bonded systems : from peptide dynamics to the function of Bacteriorhodopsin Paris-6 University, France. Under supervision of Prof. Jeremy C. Smith and Prof. Paul Vigny. Research Interests: Computational Chemistry, Drug Design and Molecular Modeling of Biomolecules. Functional Genomics/Proteomics: from protein sequence to function and structure. Structure and Function of an integral functional biomolecular unit in its natural environemnt. Free Energy Calculations. Computational drug discovery: Combinatorial library design, diversity/similarity characterization, binding site characterization, virtual docking, QSAR and HT-'Binary'-QSAR. Links to public and private biotech sites.

66. Bentham Science Publishers Ltd. Home Page Protein and Peptide Letters publishes short papers in all important aspects of protein and peptide research, including structural studies, recombinant expression, function, synthesis, enzymology, immunology, molecular modeling, drug design etc. http://www.bentham.org/ppl/index.html

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67. CAChe Molecular Modeling Tutorial http://www.chem.ox.ac.uk/course/cache/default.html

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68. Molecular Modeling Glossary In Silico molecular modeling glossary Evolving terminology for emerging technologies Suggestions? Comments? CAMM See Computer Assisted molecular modeling. http://www.genomicglossaries.com/content/molecular_modeling_gloss.asp

You are here Genomic Glossary homepage/Search In silico In Silico Evolving terminology for emerging technologies Suggestions? Comments? Questions? mchitty@healthtech.com Last revised April 21, 2004 View a Printer-Friendly Version of this Web Page! Registration policy has details Mr. Ms. Mrs. Dr. Prof. First: Last: Title: Dept.: Company: Address: City: State: Zip: Country: Email: Opt-out of Email YES NO Telephone: Fax: document.FrontPage_Form1.interest.value = 'ISB'; An understanding of the behavior of biological systems at each level of their organization can only be achieved by careful study of the complex dynamical interactions between the components of these systems. For this understanding to be quantitative it is necessary to develop structurally, biochemically and biophysically detailed mathematical models. Once developed, these models can be simulated, analyzed, and visualized through application of modern engineering and computational approaches. IBM, Functional Genomics and Systems Biology Overview http://www.research.ibm.com/FunGen/index.html

69. QuantumBio Inc -- A Next Generation Of CAMM & CADD Develops solutions for ComputerAssisted molecular modeling and Computer-Assisted Drug Design, with emphasis on semiempirical quantum mechanics and bioinformatics. http://www.quantumbioinc.com/

A Quantum Breakthrough in Drug Discovery Home About Us Solutions Products ... Events in Digital Briefs, October 6, 2003 [2003, 81 (40), 32-34] and HAMStER presented at 226th ACS National Meeting, Sept 7-11, 2003 Pennsylvania's Ben Franklin Technology PArtners (Central Region) awards a phase 1 investment in QuantumBio. QuantumBio, Inc is accelerating the drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations a next generation of Computer-Assisted Molecular Modeling (CAMM) and Computer-Assisted Drug Design (CADD) solutions. QuantumBio's CAMM/CADD software and data content is based on technology developed between 1995 and the present in the Department of Chemistry at the Pennsylvania State University in the labs of Dr. Kenneth M. Merz, Jr ., an international leader in the field of computational chemistry for drug discovery. These proprietary tools developed at the cost of scores of FTE years and millions of dollars at Penn State will enable scientists engaged in drug discovery to leverage the precision of quantum mechanical approaches to model interactions between proteins and small molecules. Medicinal chemistry is an integrated part of the drug discovery process. Medicinal chemists discover and optimize new chemical entities (NCE) to ensure a portfolio of high quality proprietary drug candidates.

70. Computational Chemistry Resources On The WWW Directory of links related to computational chemistry. Offers several tutorials for understanding the basics of molecular structure and molecular modeling techniques. http://www.chem.swin.edu.au/chem_ref.html

WWW Computational Chemistry Resources This list of resources is designed to provide computational chemists, students and other people interested in the CAUT Computational Chemistry project with a list of useful web sites related to computational chemistry and molecular modelling This list is not intended to be a definitive list of chemistry pages on the web, but rather to provide links to some of the more most useful sites on the Web. Please let us know of any changes or suggestions for this list. The resources are divided into: General chemistry Chemistry education Computational chemistry Resources Molecular modelling ... The URL update form Interesting general chemistry resources The Australian Chemistry Network Beilstein Information Systems The Free University, Berlin Chemistry Index (very comprehensive) The Yahoo Chemistry Index Chemistry Databases Links for Chemists; University of Liverpool including World Wide Web Virtual Library: Chemistry The Information Retrieval in Chemistry The SDSU Chemistry Information Reference Silicon Graphics' Chemistry and Biological Sciences resources WebElements - The periodic table via WWW MIME types for Chemistry Network Science - an electronic journal for those in the chemical, pharmaceutical and biotechnology industries

71. ChemSW Chemistry Software For Windows Offers commercial chemistry software for inventory management, chromatography, mass spectrometry, molecular modeling, physical properties, reaction kinetics, and radioactive decay. http://www.chemsw.com/

The Leading provider of chemical inventory Management systems, MSDS systems and chemistry laboratory Software. ChemSW is the leader in asset management software for laboratories worldwide, providing inventory and laboratory solutions since 1991.  Our software is installed in thousands of laboratories including the smallest of chemical stockrooms and the largest enterprise environments. We pride ourselves in the best customer service and support available and our knowledgeable staff will be glad to assist you in solving any of your laboratory software needs. Request a free demo CD of our products to see how we can solve your laboratory software needs. Click here! To find out more about how we can meet your chemical inventory management challenges, call us today. We'll arrange a personalized web demonstration. 707-864-0845 Unsubscribe (check box and enter e-mail) ANNOUNCING A FREE CISPro Chemical Inventory System seminar! Please join us for a free, half-day seminar and learn about new tools for accurately tracking and managing your chemical inventory and hazardous materials.

72. Molmod2.chem.georgetown.edu/ Center for molecular modelingCMM Home Research People Publications Links Resources Contact the CMM. http://molmod2.chem.georgetown.edu/

73. DDL Main Page molecular modeling resources, software and projects. Home of the programs Vega and BioDock. http://users.unimi.it/~ddl/

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74. Chemistry - Links For Chemists - Reference - Molecular Modelling Molecular Models (Solid 3D models) @ 3D Biochem Inc. US; The molecular modeling Electronic Conference TMMeC MY; The QSAR and Modelling Society @ ETH Zurich CH; http://www.liv.ac.uk/Chemistry/Links/refmodl.html

Links for Chemists Chemistry section of the WWW Virtual Library Virtual Library Science Chemistry : Molecular Modelling / Visualisation Resources 3D Molecular Designs US 3D Molecular Modelling @ Toyaku JP 3D Molecules @ Crete GR FR C4: Computers in Chemistry at Cabrillo College (Molecular visualization) @ Cabrillo College US Chemie in vier Dimensionen @ Saarland DE Chemistry Pictures @ Swedish University Network SE ChemVisu @ Friburg CH Chemist's Art Gallery @ CSC FI Chemical Bonds, Molecular Shapes, and Molecular Models @ Eastern Oregon US ChemVis: Chemical visualization on the Internet @ Erlangen DE ChemViz - Chemical visualization @ NCSA US Chime Pages @ Dublin City IE Chime Resources @ Uni. Massachusetts US BioMolecular Tutorials in Chime @ Erlangen DE Crystal Structures of Minerals @ Manchester UK ExPASy (Protein modelling) CH Garlic (Free Molecular Visualization Program) HR @ Pittsburgh US Ghemical (Unix based freeware molecular modelling package) @ Kuopio FI HyperChem Mailing List @ HyperChem Inc. US IMB Jena Image Library of Biological Macromolecules @ Jena DE Indiana University Molecular Structure Center @ Indiana US Indigo Instruments (Molecular models) US Introduction to Computational Chemistry (Book by Frank Jensen) @ Odense DK Introduction to Molecular Modelling @ Brunel UK Java Chemical Sample 3D Molecule Structure Viewer US Library of 3-D Molecular Structures @ NYU US MacroModel @ Columbia US MathMol (Mathematics and Molecules) @ NYU US Med. Chem. Feature Molecule

75. 3D Genoscience - Drug Discovery And Development Of Molecules To Fight HIV And He Genmol is a 3D molecular modeling software for measuring resistance/affinity between a ligand and a target, used for Disease Management, Drug Discovery and Development of molecules. http://www.3dgenoscience.com/index.php

Genoscience 23 rue de Friedland 13 006 Marseille France Tel : +33.4.91.25.95.14 Fax : 33.4.91.79.20.44 Genoscience is an early-stage biotechnology company, which aimed at developing new potent drugs against viruses, such as HIV and HCV . The research uses a unique 3D molecular modelling software that provides innovative solutions to discover and develop novel drugs to fight viruses. Genoscience has developed a virtual screening platform that allows screening of large libraries (over 2M) of potential drugs over a targeted protein (or entire families of related proteins). Virtual hits –from 1 to 2,000- could be selected, purchased (generally within 6 weeks) and experimentally tested. HIV/HCV market opportunity : A family of HCV protease inhibitors was generated by drug design, among which fifteen molecules were found to be highly active in vitro with a activity at nanomoles ( PCT Patent ). Two compounds with potent antiviral activities against HIV and HCV were obtained from a plant, with a commercial exclusivity for Genoscience Introduction of our technologies by Dr Mark Wainberg : "Solutions for Disease Management and Development of Drugs to Fight Viruses" in the section " our technologies I Welcome I I Meet the company I I Our Technologies I I Our Products I I Investors Information I I In the News I I Join Our Team I I Contact us I Terms of Service Designed and Produced by E-MedHosting.com

76. Index Of /hypermail/MOLECULAR-MODELLING molecular modeling LaboratoryHome Page The molecular modeling laboratory provides students, staff, and faculty the ability to build and graphically manipulate 3-D images of complex molecules such as http://www.bio.net/hypermail/MOLECULAR-MODELLING/

molmodel/bionet.molec-model Newsgroup Archive And now, a word from our sponsors... Please contact biosci@net.bio.net if you wish to advertise in this space. BIOSCI Home Page molmodel Charter Other Newsgroups BIOSCI Documentation ... Post a new article to molmodel/bionet.molec-model via the BIOSCI mail-Usenet gateway. Read the most recent molmodel/bionet.molec-model articles This archive is broken down by year (YYYY) and month (MM) The articles are stored in directories named molmodel.YYYYMM and are listed below the search box. This archive is indexed using Excite. To search for a keyword or phrase occurring in the molmodel/bionet.molec-model newsgroup, enter your query below. Search For: It's best to enter words or simple phrases. You can use Boolean operators (AND, OR, NOT) and parentheses to narrow the search, and prepend search words with a + sign (or - sign) to require (or exclude) words from the search. On the results page, you can click on the and icons next to each returned "hit" to look for other similar pages. More Search Help Name Last modified Size ... Parent Directory 25-Apr-2001 16:14 - molmodel.200406/

77. Molecular Modelling Toolbox XMol User Guide. Other Links of Interest. The NIH molecular modeling Home Page The Cambridge University molecular modeling Teaching Laboratory. http://webnet.mednet.gu.se/chemistry/molmod/

HTTP 200 Document follows Date: Sun, 06 Jun 2004 11:55:59 GMT Server: NCSA/1.5.2 Last-modified: Sat, 27 Mar 1999 01:41:12 GMT Content-type: text/html Content-length: 4263 Molecular Modelling Toolbox General Documents The NIH Guide to Molecular Modelling is a comprehensive introduction to computational chemistry. Getting Started Molecular Mechanics Quantum Mechanics References Structure Databases Klotho , the biochemical compounds declarative database, is a collection of molecules of interest to the computational biochemist. Search the Protein Data Bank with a graphical interface or use PDB At A Glance , a hypertext-based table of contents from NIH . If you need to access the latest version of the database, try the webserver at the Brookhaven Laboratory Structural Classification of Proteins (SCOP) is a WWW-service with PDB entries listed in the context of secondary/tertiary structure from University of Cambridge SWISS-3DIMAGE is a database of annotated 3D images Amino acids Basic biomolecules , required knowledge for 1st semester students at the medical faculty A large collection of structure databases and other modelling resources is maintained by NIH Online User Manuals The Cambridge Structural Data Base Web manual , contact Staffan Sundell for information on how to access the CSD software.

78. Mathub - The Focal Point For Computational Materials Science On The Web By Micha Features current and background information about molecular modeling and informatics for chemistry and materials science. http://www.mathub.com/

ABOUT MATHUB REGISTER SITE MAP CONTACT US About Mathub Mathub is the focal point for computational materials science on the web, providing a gateway to scientific information about modeling and informatics. If you're interested in in silico materials science this site is just what you've been looking for. Register Free registration is required to access the Mathub site. Register now Features Modeling at Continental Tire - an Interview Computational Chemistry in the Fine Chemicals Industry Theoretical and Computational Chemistry at University College London Nanoscale Modeling. More Features... Job Vacancies March 2004 - Graphic Design Specialist - Cambridge, UK. Full time. Contact Michael Francis WebWatch WebWatch reviews the best of the web for computational materials science. Current Mathub WebWatch is

79. SWBIC - Molecular Modeling & Visualization molecular modeling Visualization. of Geneva A site covering the basics of molecular modeling and image rendering techniques. more info10121. http://www.swbic.org/links/1.13.php

iDNAfication - Solve mysteries using forensic techniques. DoD Biotech Resources Minority Student Resources Bioinformatics Tools Search Internet Resources ... Sites with Multiple or Integrated Tools Opens resource in a 2nd browser window. a la mode: A Ligand and Monomer Object Data Environment [The Nucleic Acid Database Project] An environment for building models of ligand and monomer molecular components. [more info] B Molecular Modeling [Scripps Institute] Formerly called Biomer, this Java applet builds molecular models to order. Designate components like DNA bases and amino acids to assemble into one molecule. The program also offers functions for energy minimization and molecular dynamics. [more info] Center for Molecular Modeling [NIH] CMM is a major supplier of molecular modeling resources and expertise to the NIH research community. The site contains many annotated links to bioinformatics resources and tutorials. [more info] ChemDraw [CambridgeSoft] ChemDraw includes stereochemistry recognition and display, multi-page documents, ChemNMR with spectral display, and Name=Struct for instant structure generation. AutoNom creates IUPAC names from structures. ChemDraw for Excel brings chemistry to Excel. The Online menu links to ChemACX.Com for easy chemical sourcing and ordering. The ChemDraw Plugin adds chemical intelligence to your browser for querying databases and displaying data from web sites. [more info] DDL - Drug Design Laboratory [Milan University, Italy] This site presents downloadable programs for drug design, including molecular dynamics for solvated molecules, program Predator to predict secondary structure of proteins, and molecular orbital calculations.

80. Molecular Mechanics A tutorial published by the Center for molecular modeling of the U.S. National Institutes of Health. http://cmm.info.nih.gov/modeling/guide_documents/molecular_mechanics_document.ht

Molecular Mechanics Background The "mechanical" molecular model was developed out of a need to describe molecular structures and properties in as practical a manner as possible. The range of applicability of molecular mechanics includes: Molecules containing thousands of atoms. Organics, oligonucleotides, peptides, and saccharides (metallo-organics and inorganics in some cases). Vacuum, implicit, or explicit solvent environments. Ground state only. Thermodynamic and kinetic (via molecular dynamics ) properties. The great computational speed of molecular mechanics allows for its use in procedures such as molecular dynamics, conformational energy searching, and docking, that require large numbers of energy evaluations. Molecular mechanics methods are based on the following principles: Nuclei and electrons are lumped into atom-like particles. Atom-like particles are spherical (radii obtained from measurements or theory) and have a net charge (obtained from theory). Interactions are based on springs and classical potentials. Interactions must be preassigned to specific sets of atoms.

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