Examples in this section are bundled with Protein Explorer.
- Antibody 2G12:
A novel domain-swapped antibody structure.
This is the first PiPE I prepared in the current PiPE format
(in which the contents were
specified in the PDB file
It is not intended to be a self-explanatory tutorial,
because I used it to illustrate an immunology journal club talk given in
September, 2003. My static slides were in this
I switched back and forth between the slides and the rotatable PiPEs.
- Structural Bioinformatics:
Slides to introduce structural bioinformatics to
a graduate-level bioinformatics class in a single lecture.
There are two PiPE chapters under What are 3D structure data?.
They deviate from the
when pressed out of order, some buttons give incorrect images.
This is because the scripts were written hastily by hand before
the PE Recorder was available.
- ConSurf Server Examples:
The ConSurf Server colors amino acids in a 3D protein structure
by evolutionary conservation -- entirely automatically.
The molecular view resulting from a ConSurf run
can be saved as a specialized PiPE. These examples are
PiPEs saved from ConSurf.
To create your own PiPE, see the
using this template:
- Empty Working Template:
Includes or illustrates all supported PiPE options, including pop-up
details, and changing the PDB file within a chapter.
The examples in this section were developed independently of PE and
are not bundled with it (but can be
The examples below are in obsolete PiPE formats and are not guaranteed to work:
- Ribosome structure/function
is covered at several levels in
by Wayne Decatur (UMass, Amherst).
Some were used to illustrate a
in Trends Biochem. Sci..
- These Historic
Examples have excellent scientific content, but were developed in 1999-2000
using obsolete PiPE formats (with
un-released experimental versions of PE) and have not yet been ported
to the current PiPE format. They include:
- Human Retinoid X Receptor Ligand-Binding Domain (by Tanapat Palaga)
- Exploring structure and function of FtsZ, a prokaryotic cell division protein and
tubulin-homologue (by Gabriel McCool)
- Structure of the Simian Virus 40 Capsid (by Stefan Welte)
Feedback to Eric Martz.