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These are the softwares that are useful
in cheminformatics
SMILES - Reactions &Molecules
SMARTS - Patterns
SMIRKS - Transforms
Softwares from Cambridgesoft
Web Tools
There are an increasing number of chemistry
oriented tools available for the Web which address three general areas. This
listing will be updated as new Web sites are brought online.
- Structure drawing
- Structure viewing
- Information searchers
Web-oriented structure drawing programs are
considered to be those which provide the ability to output a gif/jpeg formatted
file. Current programs which provide this level of functionality include:
Web-oriented structure viewing programs are
those which provide the ability to view 2D and 3D structures on the Web. In
general, all of the current programs evolved from
RasMol, the molecular visualization program
developed by Roger Sayle. RasMol was developed to visualize and generate
publication quality images of proteins, nucleic acids and small molecules. It
was developed at the University of Edinburgh's Biocomputing Research Unit and
the Biomolecular Structures Group at Glaxo Research and Development, Greenford,
UK. RasMol reads several formats of molecular co-ordinate files and
interactively displays the molecule using a variety of color schemes and
representations. Molecules may be rotated, translated, zoomed, z-clipped (slabbed)
interactively. Rendered images 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. RasMol can be installed as a Browser
helper application so that it is activated each time that a molecular data file
is accessed. Other programs which provide this level of functionality
include:
- ChemScape Chime
(MDL Information Systems) is a browser plugin that implements RasMol
directly within the browser window. The product is available free of charge
for MacOS, Windows, and UNIX.
-
ChemSymphony (Cherwell Scientific) is a platform-independent set of
interactive JAVA applets that allows 3-D molecular structures to be easily
incorporated into HTML documents. The system understands most of the common
file formats. Structures can be manipulated in real time, rendered in a
variety of styles, and then edited by the user. Unlike traditional viewers
which run as helper applications under the browser, ChemSymphony is a set of
applets which are downloaded when a page is viewed. Thus, the Web site must
subscribe to ChemSymphony and imbed the applet commands in the HTML of the
page being served in order to utilize these features.
- CS ChemOffice
Net(CambridgeSoft) is a subset of CS ChemOffice Pro which will allow
viewing of the chemical structures and molecular models available at the
ChemFinder WebServer and at other sites on the Net. Since CS ChemOffice Net is
a suite that contains CS ChemDraw Net and CS Chem3D Net, it combines features
of a viewer and a Net-based structure editor.
- The Molecular
Inventor (Tripos, Inc.) is a Netscape Navigator plugin which provides
interactive 3D molecular visualization for Silicon Graphics Workstations. The
plugin is distributed free of charge as an unsupported product. Tripos also
provides Web-based products which interface their product line through the
Discovery.Net Club - a fee-based service.
- WebLab Viewer
(Molecular Simulations Inc.) is the component of WebLab which provides
molecular visualization. It runs as a separate application on a PC, Mac, or
UNIX system and interacts with the browser, working as a helper application.
Because WebLab Viewer is a separate application, it can also be used
independently of the Web to visualize molecular structure files. The Viewer
has all the properties of a standard desktop application. It is compatible
with Microsoft's OLE2 standard. This means that you can paste a molecule from
the Viewer into an application like Word or PowerPoint. The molecule will
appear as a picture, but double-clicking on the picture runs the Viewer within
the other application - allowing you to rotate and view the 3D structure in a
word processor or DTP package. Users who want extended functionality - such as
molecular sketching and optimization of molecular structures - will be able to
purchase WebLab Viewer+ towards the end of 1997.
Finally, there are several information
searchers and data sources which have been given Web interfaces. These include:
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