| Although
designed for University level research, the following software packages are ideal
to supplement high school and advanced middle school chemistry lessons. The software
can also be used as a tool for student science projects. These
are all 'free software programs', although many require registration. Chime
is a plug-in program that allows you to view molecules in 3-D via Netscape or
Explorer browsers. Although Chime is free you will have to register to download
the version from MDL.
RasMol
(Recommended for K-12 Applications)RasMol
is a molecular graphics program developed at the University of Edinburgh. The
software is intended for the visualization of proteins, nucleic acids and small
molecules. The program has the ability to read in PDB as well as several other
formats. For more information on RasMol visit the RasMol
Home Page.
Swiss-PdbViewer
is an application that provides a user friendly interface allowing to analyze
several proteins at the same time. The proteins can be superimposed in order to
deduce structural alignments and compare their active sites or any other relevant
parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy
to obtain thanks to the intuitive graphic and menu interface.
ArgusLab
ArgusLab contains: An interactive 3D molecule builder that allows the user to
build and manipulate complex structures; and, a rich suite of computational methods,
both quantum mechanical and molecular mechanical, for calculating ground and excited
states properties. The program is free for academic use
http://www.planaria-software.com/
MAGEMage
requires the use of Kinemage files. There are presently available a large number
of these files for both education and research purposes (see the Kinemage
Home Page for more information. ) You can now run Kinemages on your home page
using a Java enabled
Mage. Because of the large number of Kinemage files available to the public
this makes for an interesting teacher tool.
eChem
is a simplified and learner-centered design version of professional visualizing
tools. It allows students to build and manipulate three-dimensional models of
molecules with a visualizer module. It also allows students to compare computationally
predicted properties of the molecule with properties they observe in the laboratory
JME
Molecular Editor is a Java applet which allows to draw / edit molecules and reactions
(including generation of substructure queries) and to depict molecules directly
within an HTML page. Editor can generate SMILES or MDL mol file of created structures.
You can download a copy at the JME
Site.
Chemis3D,
Molecular viewer is a Java Applet which renders virtual 3D molecular models within
a Web document. It is specially designed for open interactive molecular visualization
on the Internet or via an intranet. Chemis3D is a small applet (~30Ko) running
well on any Java-enabled browser and requiring no specialized plug-in nor professional
applications.
The
TINKER molecular modeling software is a complete and general package for molecular
mechanics and dynamics, with some special features for biopolymers. TINKER has
the ability to use any of several common parameter sets, such as Amber (ff94,
ff96, ff98 and ff99), CHARMM (19 and 27), Allinger MM (MM2-1991 and MM3-2000),
OPLS (OPLS-UA, OPLS-AA and OPLS-AA/L).
YASARA is a molecular-graphics,
-modeling and -simulation package for Linux and Windows.YASARA is powered by PVL
(Portable Vector Language), a new development framework . PVL allows you to visualize
even the largest proteins and enables true interactive real-time simulations with
highly accurate force fields on standard PCs. The initial level stage can be downloaded
free. | 
