Difference between revisions of "Websites Using Jmol"

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* [http://people.biochem.umass.edu/fournierlab/snornadb/ Yeast snoRNA Database] - University of Massachusetts, Amherst. ''A comprehensive database of S. cerevisiae H/ACA and C/D box small nucleolar RNAs.''
 
* [http://people.biochem.umass.edu/fournierlab/snornadb/ Yeast snoRNA Database] - University of Massachusetts, Amherst. ''A comprehensive database of S. cerevisiae H/ACA and C/D box small nucleolar RNAs.''
 
* [http://zinc.docking.org/ Zinc is not Commercial] - University of California, San Francisco, USA Database with more than 3.3 million 3D small molecules free for download and online viewable with Jmol
 
* [http://zinc.docking.org/ Zinc is not Commercial] - University of California, San Francisco, USA Database with more than 3.3 million 3D small molecules free for download and online viewable with Jmol
 +
* [http://chemweb.chem.fsu.edu/editors/rlight/polyhedra/index.html Polyhedra structures] Links to the five Platonic solids and to a truncated icosahedron, all with colored faces, and a link to the C60 buckminsterfullerene structure.

Revision as of 18:39, 18 October 2007

Jmol/JSmol Applications

Jmol users, please add your (X)HTML website here.


  • 3Dchem.com The Molecule of the Month website from the University of Oxford, now updated to make use of Jmol, showing hundreds of small molecules, inorganic polyhedra and protein structures - Karl Harrison, Oxford, UK.
  • Aptanomics Intranet The Jmol applet is used to explore the structure of molecules in our database. - Aptanomics SA, Lyon, France.
  • Apuntes de Biología Molecular by M. Gonzalo Claros - Universidad de Málaga, Málaga (Spain).
  • Atlas of Macromolecules is a browsable list of over 150 3D protein or nucleic acid structures, many with snapshots, and each with links for viewing in FirstGlance in Jmol.
  • Banco de Datos de Moleculas Interactivas is an undergoing project to provide High School and Higher Education Students and Teachers with tools to develop a throughly chemistry teaching experience.-in Spanish, by Einar Coutin, Universidad de Los Andes (Venezuela).
  • Biochemistry for Medical Students--Protein Structure and Function Examples of protein structures relevant to medicine. --Eric Walters, Rosalind Franklin University of Medicine and Science (USA).
  • Biomodel Teaching resources and self-guided learning for structure and interaction of biomolecules: amino acids, carbohydrates, stereoisomerism, lipids, lipid bilayer, proteins, nucleic acids, nucleic acid-protein complexes, biopolymers - in Spanish, by Angel Herraez, Universidad de Alcalá (Spain).
  • Biomolecular Explorer 3D designed to give high school biology teachers easy access to interactive 3D structures of biologically significant molecules. Website and CD-ROM.
  • Biomolecules at Kenyon Jmol tutorials created by Kenyon College undergraduates.
  • BioROM Ayudas para el aprendizaje de bioquímica, biotecnología y biología molecular - Material in Spanish, a collaboration among several universities from Spain and Chile. Website and CD-ROM.
  • Bioquímica e Biologia Molecular - Centro de Biotecnologia e Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul - Porto Alegre - Brazil (in portuguese)
  • Biotopics 3-D structures of simple Biological molecules - carbohydrates, lipids, nucleic acids, other compounds of Biological interest.
  • BioWiki Wiki with Jmol applet - users can place 3D-molecular models anywhere in this wiki easily.
  • Browser-linked Chemkin-style thermodynamic database Demo for linking chemical nicknames & structures without altering a legacy database.
  • ChemExper Chemical Directory A database containing over 500000 molecules, 10000 IR and 70000 3D models that can be visualized using Jmol.
  • CDK Web Show case for functionality in the Chemistry Development Kit. The website uses Jmol for generated rendering 3D structures.
  • Chlorine Atomic Orbitals - Hosted by the University of Wisconsin Oshkosh this web page allows the user to display up to 4 atomic orbitals in Jmol. Perl scripts for generating pages like this will be made available soon (2006/05/22).
  • Conformational Epitope Prediction Server - Bioinformatics Centre, University of Pune, India. Shows predicted surface antigenic epitopes in Jmol.
  • CoolMolecules - St. Olaf College, USA
  • Data Book of Molecules - Home Page for Learning Environmental Chemistry, Japan
  • Dr. Gutow's VSEPR Tutorial - Hosted by the University of Wisconsin Oshkosh this is a tutorial on the VSEPR (Valence Shell Electron Pair Repulsion) model for determining molecular shapes. Example molecules viewed using Jmol.
  • DCU CHIME and Jmol Pages - Dublin City University visitor access page to Molecular Viewing Galleries and organic chemistry tutorials.
  • Dutch Dictionary on Organic Chemistry - Radboud University Nijmegen, The Netherlands
  • EDinformatics -- Explain it With Molecules This is an interactive site designed for K-12 students.
  • Evolution of Knowledge Uses scripts to color conserved amino acids in proteins like insulin and G3PD. Attention: this is an "intelligent design" website that links to non-peer reviewed material. The arguments for intelligent design of macromolecules and of life in general are very weak and have been refuted in many venues. Note that the chapters of the book that this site links to have not been subject to legitimate peer review.
  • FirstGlance in Jmol is a simple, browser-based tool for molecular visualization. Buttons show informative views of any macromolecule available on-line. Help, including color keys, appears automatically and is always in view. Hyperlinks show a molecule in one click. It is designed to be useful both to novices and to specialists.
  • FlexWeb - FIRST Online - Arizona State University, Tempe, Arizona, USA; FIRST / FRODA Software for rigidity analysis and geometric rigidity simulation. Registration Required but free for non-commercial users
  • FXI Deficiency Mutation Database - UCL, UK
  • GRIS: Glycoprotein-hormone Receptors Information System - GRIS gathers and presents heterogenous data on glycoprotein-hormone receptors (GpHRs) such as mutational data, homology models and allows the users to employ several structural analysis tools. Jmol is used to visualize the models.
  • IMGT/3Dstructure-DB: IMGT® (http://imgt.cines.fr) is the international ImMunoGeneTics information system, an integrated knowledge resource specialized in the immunoglobulins, T cell receptors, major histocompatibility complex and related proteins of the immune system.
  • Inorganic Crystal Structure Database (ICSD) is the world's most extensive database of inorganic crystal structure data. It is produced by the Fachinformationszentrum FIZ Karlsruhe in Europe and the U.S. National Institute of Standards and Technology NIST, with the WWW and Jmol interface developed at the Institute Laue-Langevin ILL in France.
  • Jena Library of Biological Macromolecules (JenaLib) - Jena, Germany
  • Librairie de molécules - Molecular model library for science secondary teachers in french, France
  • Modeome3D database - Homology 3D-models database with Jmol integrated tools.
  • Mol4D - CMBI, Radboud University Nijmegen, The Netherlands Tutorials Organic Chemistry and Molecule editor/Mopac interface.
  • Molecular Origami Precision Scale Models from Paper. View the model using Jmol or make it out of paper yourself. - St. Olaf College]
  • Molecular Structure of Hormones in the Human Body (Medical Computing .Net) - Irvine, USA
  • Moleculen in Beweging - CMBI, Radboud University Nijmegen, The Netherlands Very nice Dutch website for high school students on several aspects of chemistry. I especially liked the IR section which links peaks to actual vibrations.
  • Molécules en 3D dossiers profitant des fonctionnalités de l'applet Jmol et utilisables par les élèves de second cycle (seconde, première, terminale) de l'enseignement français (dossiers adaptés aux programmes français en vigueur).
  • Molecules In Motion molecular animations - Interactive Molecular Structures
  • Molecule of the Month at Bristol University Interesting facts about molecules written by contributors from all over the world.
  • MolVisions Custom physical models of molecules.
  • MolviZ.Org offers tutorials on DNA Structure, Hemoglobin, Lipid Bilayers and Channels, Collagen, and other Jmol-based and cross-platform resources for education and research.
  • MSD ligand chemistry - European Bioinformatics Institute, UK
  • Nanocrystal Visualization Tool - Web interface for the visualization of semiconductor nanocrystals - University of Naples, Italy.
  • NASIM/VPL - University of Technology, Bratislava, Slovakia NASIM/VPL - Nanotechnology Simulator / Virtual Physician Laboratory is a opensource initiative of CCMS laboratory built on top of Jmol and other projects that provides to construct simple molecules with interactive editor and compute problems from chemistry on computer clusters.
  • NeuroMouse - University of Toronto; Toronto, Canada. Neuromouse - is an interactive object-oriented database of information on the mouse nervous system. Jmol viewers are employed to allow users to visualize key proteins in important signal transduction pathways such as those which govern the process of programmed cell death (apoptosis).
  • OCA - OCA, a browser/database for protein structure and function at the Weizmann Institute, Israel and several mirror sites around the world; offers a convenient interface for searching the Protein Databank (PDB) and uses Jmol to show results.
  • Orbitron - The Orbitron: a gallery of atomic orbitals and molecular orbitals on the WWW by Mark Winter at the University of Sheffield, UK: includes dot-density plots rendered in Jmol for the display of atomic, hybrid, and a few molecular orbitals
  • Online Macromolecular Museum - CLU, Thousand Oaks, CA, USA The OMM contains exhibits of a variety of macromolecules. New exhibits use Jmol. Older, Chime-based exhibits are being converted to Jmol. One exhibit is an interactive Jmol scripting tutorial.
  • p53 Knowledgebase - Bioinformatics Institute (Singapore)
  • PDBsum - European Bioinformatics Institute, UK
  • Protein Data Bank Research Collaboratory for Structural Bioinformatics Protein Data Bank now uses Jmol as one of its primary viewers
  • Protein Dipole Moment Server - Weizmann Institute, Rehovot Israel With this server you can discover if your protein might have an unusally large net charge or dipole moment, and how this might relate to specific structural features of the protein, and thereby its function.
  • ProteinExplorer.Org - A powerful software package to help explore and understand macromolecular 3D structure, with levels for beginners and experts. Although it works primarily with Chime, molecular views can be exported to MolSlides that use Jmol.
  • Protein Structure Annotation Database A database of protein structure annotation that uses the Jmol applet as really nice tool for displaying the structure of proteins.
  • QCRNA The DFT Database for RNA Catalysis is a large collection of high-level density-functional electronic structure calculations of molecules, complexes and reactions relevent to RNA catalysis.
  • RESP ESP charge DDataBase, R.E.DD.B. - Université de Picardie Jules Verne - Burnham Institute for Medical Research
  • Structure and reaction mechanism of RUBISCO A Rubisco tutorial with a Jmol version.
  • Protein Workbench STRAP Simultaneously displays sequence alignments and 3d-Structures.
  • Science Stuff, Inc. - uses Jmol to present 3-d structures of chemical compounds in their chemicals catalog.
  • Sudoku Assistant Uses Jmol to visualize the three-dimensional logical chains of Sudoku puzzles.
  • Symmetry Resources at Otterbein - includes Symmetry Tutorial, an introduction to point group symmetry that uses Jmol to visualize symmetry elements and operations, and The Symmetry Gallery, an interactive collection of over 60 unique molecules with interactive display of all symmetry elements and animation of all operations. (Outstanding animated effects!)
  • The Virtual Museum of Minerals and Molecules - Previously implemented on Chime, the VMMM is now fully converted to Jmol (applet + JavaScript), with over 100 molecules and minerals in its galleries.
  • TLS Motion Determination - University of Washington, USA Analyzes a protein crystal structure for evidence of flexibility. Animations of the predicted flexibility are presented using Jmol.
  • Transporter Library The Transporter Ligand Library, created by Dept. of Neurochemistry, CRC, HAS collects biological and structural information about ligands for neurotransmitter transporters. - Budapest, Hungary
  • Undergraduate Education - Ohio State University, USA A collection of online educational material for Chemistry. The main focus is on Organic Chemistry but there are also materials for General Chemistry. Many areas use Chime, but I am converting to Jmol.
  • U Penn X-ray Facility - The X-ray Facility in the Department of Chemistry at the University of Pennsylvania uses Jmol to archive completed structure determinations
  • Virtual Textbook of Organic Chemistry - Michigan State University, USA Because this is a large site the Jmol references may be difficult to find ... but they are in there.
  • World Wide Molecular Matrix - Unilever Centre at Cambridge, UK (2006/04/12 file not found)
  • XdomView - National University of Singapore
  • Yeast snoRNA Database - University of Massachusetts, Amherst. A comprehensive database of S. cerevisiae H/ACA and C/D box small nucleolar RNAs.
  • Zinc is not Commercial - University of California, San Francisco, USA Database with more than 3.3 million 3D small molecules free for download and online viewable with Jmol
  • Polyhedra structures Links to the five Platonic solids and to a truncated icosahedron, all with colored faces, and a link to the C60 buckminsterfullerene structure.