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Molecule Visualization |
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Molecule Visualization |
The purpose of this new feature of the Chemistry Section Home Page is to provide faculty and students with information on retreiving, building, and displaying computer-generated two/three dimensional structures. While it is not designed as a full-featured molecular modeling or computational chemistry library, it does included references to commercial programs that can be used for simple molecular modeling studies.
Most of the software and structure libraries mentioned here are free! If you are reading this page on a computer screen, you have access to the Internet and therefore you can download any of the material discussed on this page. While any of the current Web browsers will work, Netscape seems to handle plug-in applications better than Internet Explorer (although the latter seems to handle Java acripts and applets faster). There are numerous examples you can view and download to give you an idea of what others are doing with this technology, especially in education. While the current focus of this page is on 3D structures, a library of 2D structure drawings is being developed for incorpration into lecture notes, handouts, and presentations.
Please feel free to suggest other applications, examples, or libraries. Write or email Marvin Pankaskie at the address on the main page.
What is ISIS/Draw? ISIS/Draw is a chemical drawing program used to create publication quality chemical structures and graphics using flexible drawing tools and pre-drawn structure templates and fragments. Preparing reports and presentations. Creating structure queries. Drawing structures for registration. Viewing chemical structures. You can use ISIS/Draw for these purposes and more. MDL offers this free license of ISIS/Draw for academic and personal use at home. This is not a "crippled" version, nor does it only create static GIF images. This is the complete ISIS/Draw package! Download it directly from Free ISIS/Draw License.
ChemSketch is another free modeling and drawing package that includes a few more features than ISIS/Draw. It includes a number of short-cut drawing features that can speed up the drawing of complex structures including nucleotide and polypeptide sequences. It can import and export to most of the common file formats (including MOL, CHM, SKC, and GIF, TIFF, and PCX) and includes a basic programming language module (ChemBasic) that allows the user to develop custom functions, templates, and preview windows. It also includes a 3D viewer that can be configured to work with both ChemSketch and ISIS/Draw as an add-in application. Some features are disabled in the freeware version and ACD does not provide user support unless you purchase the commercial version. Other add-on components include modules for calculating logP, logD, and pKa, an NMR/IR/MS spectrum predictor, and an HPLC/GC simulator. Users must register to download ChemSketch, but registration is free.
What is Chime? Chime is a browser plug-in that allows for the visulaization of molecular structures from within your Web browser. It is a product of MDL Incorporated and is based on the RasMol program written by Roger Sayle. Molecules, usually as 3-dimensional coordinate files such as pdb, xyz, or mol, can be viewed, dynamically rotated, sized, colored, and selected to highlight areas of interest. It is free, easily installed, and is available for both the PC and Macintosh/PPC operating systems. There are several good places to learn about using Chime, including Creating Enhanced Web Pages for Chemistry, Chime Applications, and New to Molecular Visualization? I have created other simple examples to demonstrate how you can use Chime to augment a report or "electronic lecture": one on Viagra® and one on the mechanism of aspirin.
What is WebLab ViewerLite? WebLab ViewerLite is similar in function to Chime, except that is is an external viewer or helper application - when required, it pops up a separate window containing the structure. Because WebLab ViewerLite is a separate application, it can be used independently of your web browser. WebLab ViewerLite is a free version of WebLab ViewerPro, offering visualization and limited analysis tools (molecular and torsional rotations, various display options, conversion to other file formats, and print output). You cannot build models with this version. You can, however, view models of pre-built structures, alter their representation, and cut and paste them into other applications like Word or PowerPoint.
What is RasMol? RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. The program was developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK by Roger Sayle.
RasMol reads in molecular co-ordinate files in a number of formats and interactively displays the molecule on the screen in a variety of colour schemes and representations. RasMol can read a prepared list of commands from a `script' file (or via interprocess communication) to allow a given image or viewpoint to be restored quickly. RasMol can also create a script file containing the commands required to regenerate the current image, or create a dynamic session. Finally the rendered image may be written out in a variety of formats including both raster and vector PostScript, GIF, PPM, BMP, PICT, Sun rasterfile or as a MolScript input script or Kinemage. The best site displaying the functionality of RasMol is still the "original" RasMol Home Page by Eric Martz.
What is VRML? VRML stands for Virtual Reality Modelling Language. It is a standardized format for describing three-dimensional objects as composed from 3-D primitives, such as spheres, cylinders, cubes, and pyramids. VRML documents are typically viewed using a VRML web browser, or through a VRML helper application, or more prevelantly now, using a VRML plugin. A VRML viewer renders the 3-dimensional environment specified in the VRML document and provides a number of functions to the user. The user can view the scene from an infinite number of directions, by walking or flying about and through a scene. Many VRML viewers provide joystick-like controls that simulate the operation of an airplane. Hyperlinks are accessed through the familar point-and-click operation, except that instead of text one points to a particular 3-D object, such as a sphere or a face of a cube. Some good examples are included on the Working with VRML page.
ChemSymphony is a platform-independent set of interactive Java applets that allows 3-D molecular structures to be easily incorporated into HTML documents. The structures can be manipulated in real time, rendered in a variety of styles which may be edited by the user. End users do not need a plug-in or external viewer, but do need a Java-compliant browser (e.g., Netscape 3/4 or Internet Explorer 3/4 with Java enabled) to view structures using these applets (the applet is part of the HTML page). Web site designers and developers can download a free copy ChemSymphony Lite, a group of Java class files which allows basic rendering and control. There are a growing number of interesting chemistry sites that employ Java applets and scripts, including:
- A Very Simple Example!
- ChemSymphony Applications
- The Open Molecule Foundation at the Imperial College in London
- Java-based Molecular Biology Work Bench is Professor Toldo's collection of prototypes and partially working applets, pointers to many interesting experiments
- Synthesis Planning Program (SPURT) is a reaction-based planning program that suggests synthetic routes for a structure the user draws directly inside the browser, by Bernhard Rhode at Novartis
- Molecular Simulations, Inc. are developing some cool Java applications in Chemistry and Bioinformatics
ChemWindow and ChemIntosh by Bio-Rad/Softshell
ChemDraw and Chem3D by CambridgeSoft
Alchemy 2000 and ChemPrint by Tripos
HSC Chemistry by Outokumpu Research Oy
Hyperchem by Hypercube
Chemistry 4-D Draw/NamExpert/Nomenclator by ChemInnovation
ChemSite by Pyramid Learning
Developed by Akira Dobashi's group at Tokyo University of Pharmacy and Life Sciences, this database is a excellent source of 3D structures of biologically active small molecules. You will need a copy of the Chime plug-in installed on your workstation to view 3D structures and dynamic simulations.
Developed by the Chemistry IT Centre of the University of Oxford, this site includes a variety of demonstrations, historical accounts of drug discovery, and several "hot" compounds such as Viagra® and Prozac®. You will need Chime to view the 3D structures and dynamic demonstrations.
Developed by Eric Martz's group in the Department of Microbiology at the University of Massachusetts, this is one of the largest collections of structure-related educational tutorials on the Internet (if not THE largest). You will need Chime, RasMol, and/or a VRML viewer.
On the face of it, a way to search for chemical compounds over the World Wide Web is not a novel concept. WWW-based chemical search engines have existed since at least 1995, including SciFinder Scholar and STN Easy from the Chemical Abstracts Service Academic Program. General-purpose databases of WWW contents (such as Yahoo and Alta Vista) have existed far longer. So what's the deal with this ChemFinder WebServer?
The key, you might say, is in the chemistry. It's one thing to pop over to Lycos and do a search for all references to Aluminum Hydroxide. It's another thing to actually find them, especially if the information you want is at a site in Australia under the listing Aluminium Hydroxide. Or if there is simply a passing mention of the compound with CAS RN 21645-51-2. Or a compound with the molecular formula Al(OH)3. By working from a single master list of chemical compounds, the ChemFinder WebServer avoids these problems, and lets you find the information you want, faster. In generating this database, we have also taken pains to identify and correct the obvious errors (like 'mehtyl', as well as invalid CAS RNs) that account for 3-5% of of all chemical information on the WWW. Very likely we have introduced some new and exciting mistakes of our own, but we are confident that the overall quality of the ChemFinder WebServer data far surpasses the bulk of the information that it indexes.
Because the ChemFinder WebServer is a chemical database, it can also provide information that a general-purpose WWW index cannot, including physical property data and 2D chemical structures. This information is somewhat sparse at the moment, but is very good for the several thousand most-common compounds. We are constantly working on getting more data, and we expect the ChemFinder WebServer only to keep improving. Access to ChemFinder WebServer is free, but you will need the ChemDraw WebServer plugin (also free) to create structure queries and view the results from this database. An expanded version of this database (ChemInfo) is available for a yearly subscription fee of $49.Other Molecular Modeling Resources
Databases
KLOTHO: Biochemical Compounds Database
NIH Molecular Modeling Home Page
NIH Molecular Biology Database
NLM Center for Biotechnology InformationPhysicochemical Properties
A library of over 65,000 structures containing chemical and biological data, developed by the Division of Specialized Information Services (SIS) of the National Library of Medicine. ChemIDplus is searchable by name, synonym, formula, and by substructure input (using the Chime and ISIS/Draw programs as the structure drawing interface) and is free of charge.
- A software package capable of predicting values for more than 20 physical properties for pure components and mixtures. Cranium runs under the Windows operating system, and a lite version is available free of charge.
SoftwareSeek
This is a new repository and database of freely-distributable and commercial tools for use in molecular biology, molecular modeling, biochemistry, and chemistry. The database presently has more than 1100 entries, and is supported by the software and web development firm of Genamics.com
Articles
Smith, Christopher "Seeing the Whole Picture with Modeling Software Packages", The Scientist, 12:17-19 (August 31, 1998)