182 COMPUTER HARDWARE, SOFTWARE
ACD/Name by Advanced Chemistry Development working in Windows
generates accurate systematic names according to IUPAC (International
Union of Pure and Applied Chemistry) and IUMBM recommendations on
nomenclature of organic chemistry and selected classes of natural products,
biochemical, organometallic, and inorganic compounds. A free download of
the Web version is available at http://www.acdlabs.com/products/java/sda/.
ACD/Structure Drawing Applet (ACD/SDA) is a complete structure
drawing, editing, and visualization tool written in pure Java that can be
incorporated into HTML documents. The applet can be used for composing
substructure queries to databases and visualizing results. Unlike platform -
dependent plug - ins or ActiveX controls, the applet runs in the same way on
any hardware platform or operating system — the only requirement is a Java -
compatible browser such as Netscape 4.0 or later or MS Internet Explorer 4.0
or later.
The Research Collaboratory for Structural Bioinformatics ’ Protein Data
Bank (RCSB - PDB at http://www.rcsb.org/pdb/home/home.do is the online
source for X - ray and NMR structural data. Many software programs men-
tioned in Section 4.5 include the facility to visualize imported data; however,
two free software programs operate well in this regard. One is MDL TM Chime
described previously in this section. Chime, a chemical structure visualization
plug - in for Internet Explorer and Netscape Communicator, supports a wide
variety of molecule coordinate formats, including PDB (protein data bank),
Molfi le (from ISIS/Draw), MOP (MOPAC input fi les), and GAU (Gaussian TM
Input fi les).
A good website that gives an overview of free programs available for
molecular visualization is maintained by Eric Martz at http://www.umass.edu/
molvis/martz/index.htm. RasMol, originally developed by Roger Sayles, is still
available at http://www.umass.edu/microbio/rasmol/index.html. It has mostly
been supplanted by Protein Explorer, a free Rasmol derivative with extended
capabilities, also available at the website addresses given in this paragraph.
The program allows the user to visualize macromolecular structure in relation
to function; also, it is easier to use than Rasmol, and it is more powerful and
faster.
The National Institutes of Health (NIH) Center for Molecular Modeling
(CMM), part of the Division of Computation Bioscience (DCB/CIT), displays
a molecular modeling page at http://cmm.info.nih.gov/modeling/. The CMM
software list is available at http://cmm.info.nih.gov/modeling/software.html.
One important visualization technique that users should acquire is the
ability to transform two - dimensional stereoviews into three dimensions. The
stereoviews may be found in visualization software such as MDL Chime and
RasMol. They are also found in journal articles in Science or Nature and others,
especially those describing new biomolecule X - ray crystallographic or NMR
solution structures. The following hints for learning to transform the ste-
reoviews come from the extremely helpful website http://www.usm.maine.
edu/∼ rhodes/0Help/StereoView.html.