The features supported by WPDB are divided into 2 categories, those that
have scientific merit and those considered to be computationally
New Features v2.0
For those of you familiar with WPDB v1.0 here are the new features
that have been added since v1.0. If you are new to WPDB then you may skip this
New Features v2.1
For those of you familiar with WPDB v2.0 here are the new features
that have been added since v2.0. If you are new to WPDB then you may skip this
Example - Comparison of Alpha and Beta Chains in Human Hemoglobin
At top left (WPDB window)
we see that the hemoglobin structure with the PDB code 1BAB
has been chosen. A sequence alignment between the A and B chains (Align
window) by the method of Needleman and Wunsch (JMB 48(3):
443-453, 1970) reveals a 44% similarity.
These aligned structures are then superimposed according to the method
of Hendrickson (Acta Cryst. A35:158-163, 1979)
based on their Calpha coodinates (3D view window).
The Contact map window reveals the interactions at a default cut-off
of 7 Å between Calpha atoms.
Red indicates intrachain contacts (i.e. contacts with itself) observed
in both 1BAB_A and 1BAB_B; green indicates intrachain contacts observed
in 1BAB_A only and blue - in 1BAB_B only.
This shows further details of the interaction between the A and B chains.
The Profile window has been zoomed to show the exposure according to Lee
and Richards (JMB 55:379-400, 1971)
for a segment of the aligned sequences. Red represents
both the A and the B chain; blue chain A only; green chain B only.
The Contact map window has been zoomed to show the interaction between
A further click would reveal the specific atoms in contact. The 3D view
window shows a solid representation of the molecule in a gray scale
where the darker the color the farther the residue from the viewer.
Example - Searching for Buried Residues in Lysozymes
The above shows the exposure calculated using the method of Lee and
Richards for a particlular lysozyme structure (1_LBA). A group of residues
in the region 75-85 are shown to be completely buried.
These residues are selected and then displayed in the 3-D Viewer.
The 3-D viewer can be used to call Raswin directly which in turn makes
those selected residues part of the Raswin set and are shown
here presented as a space filling representation.
Example - Thermal Motion in a Toxic Loop
Postsynaptic neurotoxins, in this case erabutoxin b,
are know to function by binding to the acetylcholine
receptor. It is believed that this occurs through the so-called toxic
loop. The residues forming this loop are highlighted in the 3-D view and
hence in the Contact map. Looking at the B factor profiles for these
residues indicates a higher thermal motion at the tip region
as one would expect.
Example - Changes in a Neuraminidase upon Antibody Binding
Two neuraminidase structures are shown, one complexed with the antibody
and one without. Arg 368 is a known mutation site and it can be seen
from the stereo 3-D view that this residue shifts significantly to
accommodate the binding.
The exact details of the shift can be seen in the Contact map.
WPDB is available
via anonymous ftp from rosebud.sdsc.edu in the directory /pub/sdsc/biology/WPDB
Building Your Own Databases
The software to build your own databases is available by contacting
one of the developers.
Developers and Version Information
Ilya N. Shindyalov Philip E. Bourne
Some of the enhancements that we are working on for v3.0 are as
follows. We welcome your input.