| 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/
MAGE
Mage 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.
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