Websites Using Jmol

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Jmol/JSmol Applications

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  • AnchorQuery Specialized pharmacophore search for targeting protein-protein interactions with MCR chemistry. University of Pittsburgh.
  • 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).
  • Arduengo Research Group X-ray Structures The Jmol applet is used to depict X-ray structures obtained by the research group of Prof. A.J. Arduengo (Structures entry under Structures Link. - University of Alabama - Tuscaloosa, U.S.A.
  • 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.
  • Biotopics 3-D structures of simple Biological molecules - carbohydrates, lipids, nucleic acids, other compounds of Biological interest.
  • BioWiki DokuWiki 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.

  • Dali - Protein structure comparison and database searching. Resulting structural superimpositions viewed using Jmol.
  • 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.
  • Dr. Gutow's Atomic Orbital Page - Hosted by the University of Wisconsin Oshkosh this site uses Jmol to allow the user to choose and compare atomic orbitals (1s, 2s, 2p, 3s, 3p, 4s, 3d and 4p orbitals).
  • Dr. Gutow's Hybrid Atomic Orbital Site - Hosted by the University of Wisconsin Oshkosh this site uses Jmol to allow the user to choose and and compare hybrid atomic orbitals. A general chemistry level explanation is also provided.
  • 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

  • EcoliWiki Wiki-based community annotation of E. coli, its bacteriophages, plasmids, and mobile genetic elements. Jmol used for visualizing proteins with available structures.
  • EDinformatics -- Explain it With Molecules This is an interactive site designed for K-12 students.
  • ePlant is a suite of 3D data display modules for integrative systems biology of the model plant Arabidopsis thaliana. Jmol is used to render annotated protein structures and protein-protein interaction networks.
  • Erowid chem compare 3d side-by-side comparison of two molecules for many, many psychoactive compounds. Features: dynamic loading of applet without page reload based on user preferences; synchronization of mouse control for both molecules; Highlighting of elements with drop-down menu.
  • 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

  • Gallixa skin cream - Gallixa is a skin product that contains gallium maltolate. A molecule of gallium maltolate is visualized in this interactive Jmol presentation.
  • GANGSTA+ - GANGSTA+ non-sequential 3D-structure alignment tool
  • 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 fully evaluated inorganic crystal structure data. It is produced by the Fachinformationszentrum FIZ Karlsruhe in Germany and the U.S. National Institute of Standards and Technology NIST, with the Jmol interface developed at the Institute Laue-Langevin ILL in France.
  • Interactive Chromatin Modeling - ICM (I see 'em) Web is the Interactive Chromatin Modeling Webserver at Bishop's Theoretical Molecular Biology Lab that allows users to fold a sequence of DNA into an array of nucleosomes or chromatin.
  • ISFI - Integrated Structure Function Innovation Website Jmol viewer in the structure gallery. The Integrated Center for Structure and Function Innovation (ISFI) is an NIH Protein Structure Initiative Specialized Center focused on developing and applying a set of synergistic technologies organized to overcome recognized bottlenecks in structure determination at the key steps of production of soluble protein and protein crystallization.

  • J-ICE J-ICE is a web-based Jmol interface forCrystallographic and Electronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), GROMOS, QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats.
  • Jena3D Viewer (Jena3D) - Jena3D is a web-based interactive viewer for three-dimensional biopolymer structures, based on Jmol. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, local structure files can be viewed. Jena3D visualizes not only information included in the PDB files but also SCOP, CATH and Pfam domains, SAPs(SNPs), PROSITE motifs and the exon structure mapped onto proteins. It is closely linked to the Jena Library of Biological Macromolecules (JenaLib).
  • Jena Library of Biological Macromolecules (JenaLib) - Integrated database on all 3D structures available at the Protein Data Bank (PDB) and the Nucleic Acid Database (NDB). Information from other databases like UniProt, PROSITE and ENSEMBL is mapped onto protein structures. For visualization the closely related Jmol based Jena3D Viewer is used. Jena, Germany
  • JnetPlus - Interactive Java viewer for visualization of network structures in form of two- or tree-dimensional graphs.

  • k-turn motifs in RNA - The Lilley lab have created a database of known and postulated k-turn sequences and three-dimensional structures. This site provides 1) a database of sequence and structure, as a resource for the RNA community, and 2) a tool to enable the manipulation and comparison of 3D structures where known.

  • Laboratório de Biologia Molecular Aplicada Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul - Porto Alegre - Brazil (in portuguese)
  • LANL Protein Feature Accent tool - The HIV database team at Los Alamos National Laboratory website now features a tool for examining the structural placement of sequence features using Jmol. Protein sequences or alignments can be submitted and will be aligned to sequences from selected HIV protein structures; sequence features in the alignment may then be selected with the mouse and corresponding residues will be highlighted on the protein graphic in the Jmol window.
  • Librairie de molécules - Molecular model library for science secondary teachers in french, France
  • La Chimie par le Web - Public courses for chemistry students - Université du Maine - France

  • Mecanismos de reacción en química inorgánica 3D-Mechanisms of Inorganic Reactions (in Spanish) - A site that presents Jmol animations of inorganic reaction mechanisms.
  • mmView Web-based viewer of the mmCIF files. - Lab. of Informatics and Chemistry, ICT Prague, Czech Republic.
  • Modeome3D database - Homology 3D-models database with Jmol integrated tools.
  • MOFomics: Metal-Organic Frameworks Characterization - Princeton University, Princeton, NJ, USA
  • Mol4D - CMBI, Radboud University Nijmegen, The Netherlands Tutorials Organic Chemistry and Molecule editor/Mopac interface.
  • Molecular Models Many models available sorted by functional group, name, or formula. A tutorial in organic nomenclature is also at this site.
  • 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.
  • Molecule of the Month at RCSB PDB Presenting short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. Same contents translated into Japanese also available from here
  • The Molmodac Project - University of Illinois A biorganic chemistry project describing the molecular mechanisms of action of a variety of small organic molecules
  • MolnQuiry Dept of Biology, Marietta College, Marietta Ohio. An educational site presenting the structural properties of biological molecules in an interactive, task-oriented learning environment
  • Molevision Molevision, to rhyme with television, is a simple site designed to help students taking their first university modules in organic chemistry.
  • 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.
  • Nano-Crystallography Open Access Database - The goal of this project is to provide 3D visualizations of crystal structures and morphologies in order to help educate future materials scientists and engineers worldwide. Portland State University
  • 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.
  • 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.
  • OrbiMol - Theoretical Chemistry Laboratory, Pierre and Marie Curie University, UPMC Paris VI / CNRS UMR 7616. Molecular orbital database for teaching, vibrations and topological approach of small molecules. [in Multi-Languages].
  • 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
  • Organic Nomenclature - Learn how to name organic molecules using the IUPAC system; learn how to recognise, draw and name stereoisomers (E/Z, R/S, M,P).

  • p53 Knowledgebase - Bioinformatics Institute (Singapore)
  • PatchFinderPlus is an automatic server to extract and display the largest positive electrostatic patch on a protein surface. Uses JmolApplet to display results.
  • PDBsum - European Bioinformatics Institute, UK
  • Periodic Table Live! - allows you to explore a broad range of information about the elements, their reactions, their properties, their structures and their histories. Hosted at the Chemical Education Digital Library
  • PocketQuery - Protein-protein interaction (PPI) inhibitor starting points from PPI structure. University of Pittsburgh.
  • 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.
  • POLYVIEW-3D - Automated annotation and visualization of macromolecular structures - University of Cincinnati and Cincinnati Children's Hospital Research Foundation, USA
  • Pore Behaviour - Explore the world of microporous materials and even fly through some of them!
  • PROPKA server PROPKA server for protein pKa predictions
  • 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.
  • Protein Workbench STRAP Simultaneously displays sequence alignments and 3d-Structures.
  • PROTEOPEDIA: The collaborative, 3D encyclopedia of proteins and other molecules

  • 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.
  • Química Orgánica en 3Dan undergoing project to illustrate different aspects of structure, stereochemistry and reactivity of Organic Molecules (in Spanish) by Carlos Valdés – Universidad de Oviedo (Spain)
  • QUIRAL Site about chirality.

  • RESP ESP charge DDataBase, R.E.DD.B. R.E.DD.B. is a database of RESP and ESP charges of high quality and reproducibility, and force field libraries for small molecules and molecular fragments: A database for computational biologists involved in AMBER/GAFF, CHARMM, GLYCAM & OPLS force field based biological studies. Université de Picardie Jules Verne - Burnham Institute for Medical Research.
  • RNA FRABASE 2.0 RNA FRAgments search engine & dataBASE - an engine with database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.
  • Romanian Database of Raman Spectroscopy This database contains mineral species (natural and synthetic) with description of crystal structure, sample image, number of sample, origin, Raman spectrum and vibrations, Raman discussion and references. Also, this site contains artefacts sample with sample image and pigment spectrum; black, red, white or blue pigment. rdrs.uaic.ro
  • Rome Center for Molecular Design RCMD - we use Jmol to view 3-D models of new potential drugs - Rino Ragno, Roma, ITA.
  • RosettaBackrub RosettaBackrub - a webserver which allows users to perform flexible backbone protein structure modeling and design. We use Jmol to visualize the structures after a backrub or protein design.

  • SChiSM2 Authoring tool: Use a web browser form to create a web page containing a series of molecular views in Jmol with buttons and descriptions. Requires knowledge of Jmol script language, but neither HTML nor javascript. You can save your project to a file and load it later.
  • Science Stuff, Inc. - uses Jmol to present 3-d structures of chemical compounds in their chemicals catalog.
  • SPPIDER - Analysis and prediction of protein-protein interaction sites - University of Cincinnati and Cincinnati Children's Hospital Research Foundation, USA
  • SSFA-GPHR - SSFA-GPHR is a database for semi-quantitative Sequence- Structure- and Function- Analysis of GPHRs - Jmol is used for structure-based searches of mutation data, visualization of single, double and triple mutations and animations of structural morphings
  • Stereochemistry - Learn how to name organic molecules using the IUPAC system; learn how to recognise, draw and name stereoisomers (E/Z, R/S, M,P).
  • Stereomutation of Pentavalent Compounds Animations of the three principal mechanisms for the interconversion of stereoisomers with a trigonal bipyramidal atom - Dr. Erik P.A. Couzijn.
  • Structure and reaction mechanism of RUBISCO A Rubisco tutorial with a Jmol version.
  • Sudoku Assistant Uses Jmol to visualize the three-dimensional logical chains of Sudoku puzzles.
  • SuperLigands - an encyclopedia dedicated to a ligand oriented view of the protein structural space. The database contains small molecule structures occurring as ligands in the Protein Data Bank. SuperLigands integrates different information about drug-likeness or binding properties. A 3D superpositioning algorithm is implemented that allows to screen all ligands for possible scaffold hoppers as well as a 2D similarity screen for compounds based on fingerprints.
  • SwarmDock Server A server for flexible protein-protein docking.
  • 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.
  • Top Five 3D Molecular Visualization Technologies for the Rest of Us - Tutorials, a Tutorial-Authoring Template, a Self-Directed Molecular Exploration Tool (FirstGlance in Jmol), a tool for Seeing Protein Evolution (ConSurf), all in Jmol, plus an easy web form for generating publication-quality custom molecular views or powerpoint-ready animations (uses PyMol).
  • TopMatch-web - Center of Applied Molecular Engineering, University of Salzburg, Austria. Public web service for the alignment and superposition of protein structures and the instant visualization of structural similiarities.
  • Transition Metal Chemistry Courses for 1st and 2nd year University students - University of the West Indies, Mona, Jamaica. Includes; coordination chemistry, crystal field theory, spectroscopy and magnetism, Java applets for display of Tanabe-Sugano diagrams and JCAMP-DX files.
  • 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

  • Virus Particle ExploreR - VIPERdb at The Scripps Research Institute. Enter the world of Icosahedral (isometric) Viral Capsids. We are interested in the study of capsid formation through the analysis of protein-protein interactions. Jmol helps visualize the symmetrical arrangements these proteins take when fully assembled into the viral capsid. It also serves as an educational tool to help understand concepts as the triangulation number (T), icosahedral symmetry, etc. To see it in action, access an entry info page for a particular virus (for example PDB-ID 2bbv) and open the IAU (Icosahedral Asymmetric Unit) tab.
  • 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.

  • 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.

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