Biomedical Engineering Reference
In-Depth Information
Rendering Tools
Most of the imaging work in bioinformatics involves data from the Protein Data Bank (PDB) or the
Molecular Modeling Database (MMDB). Searching for a structure is typically through protein name or
ID. For example, data in the PDB is accessible by name or four-letter identifier. As illustrated
Figure 5-
5
, the identifier for Glutamine Synthetase is 1FPY. Note from the summary information in PDB that
the Glutamine Synthetase molecule is represented by almost 46,000 atoms, which explains in part
why rendering the data is so computationally expensive. The resolution listed for the data—the
RMSD—is 2.89 Angstroms.
Figure 5-5. The Protein Data Bank (PDB). Here, the PDB shows summary
data for Glutamine Synthetase, and the four-letter code for the protein,
1FPY. Note that there are almost 46,000 atoms and over 5,600 residues in
the structure.
Representative protein structure rendering programs available as free downloads from the Internet
include RasMol, Cn3D, PyMol, SWISS-PDBViewer, and Chimera. A summary of the features of these
programs appears in
Table 5-2
.
Table 5-2. Application Feature Summary. Some of the more popular protein
structure rendering programs are summarized here. All of these programs
are available from the Internet at no cost for non-commercial users.
SWISS-
PDBViewer
Feature
RasMol
Cn3D
PyMol
Chimera
Architecture
Stand-alone
Plug-in
Web-
enabled
Web-enabled
Web-enabled
