Origami & Protein Related Links
Molecular Origami gets most of its spatial coordinates from the
Brookhaven National Laboratory's - Protein Data Bank
A Brief Description of the Protein Data Bank -
"The Protein Data Bank (PDB) is an archive of experimentally determined
three-dimensional structures of biological macromolecules, serving a
global community of researchers, educators, and students. The archives
contain atomic coordinates, bibliographic citations, primary and
secondary structure information, as well as crystallographic structure
factors and NMR experimental data. The PDB Newsletter and CD ROM are
published quarterly. The PDB is supported by a combination of Federal
Government Agency funds and user fees. Support is provided by the U.S.
National Science Foundation, the U.S. Public Health Service, National
Institutes of Health, National Center for Research Resources, National
Institutes of General Medical Sciences, National Library of Medicine, and
the U.S. Department of Energy under contract DE-AC02-76CH00016 and user
ExPASy - Expert
Protein Analysis System.
This is a molecular
maintained by the Geneva University Hospital and the University of Geneva
and "dedicated to the analysis of protein and nucleic acid sequences."
This server has a search called ENZYME which allows for a search of to
find all the possible names for a given compound. Swiss-Prot is a
protein sequence database within ExPASy. There is also a molecular
viewing program called Swiss 3Dimage. With this program you can look at
two dimensional picture of an protein that is colored and shaded to
SWISS-MODEL Repository is "A database of automatically generated
protein models." It warns you because it is automated the data may not
be completely reliable. Working with the data we found some bond
distances of 170 pm when they should have been more like 130 pm. Overall
though, almost all the data seems to be accurate. Coordinates are
written very similar to the Brookhaven PDB files and are also readable by
The Cambridge Crystallographic
Data Centre is a site that costs $800 per year to lease and has
over 160,000 crystal structures.
Another site to get coordinates for smaller molecules is Indiana University Molecular
Here when entering a search string you need
to enter the full name (exa. iron or Iron instead of Fe).
Be sure to check out the Java molecular modeling.
How they get their data
Researchers throughout the world submit spatial coordinates to the
various databases. The researchers obtain these coordinates mainly
crystallography or 'NMR interproton distance restraints'
Much of the PDB's data coordinates have been obtained using a program
that was written by Axel
Downloads from other sites
Download RasMol is a program
written by Roger Sayle of Glaxo Wellcome.
Users Manual is located online.
which is used to view 2D and 3D molecules.
A program called PovChem
looks like it is very similar to what Bob and I are working on. I
haven't gotten a chance to play with it yet because it needs a ray tracer
download. I have gotten to work with the initial interface and it is not
very user friendly.
The OWL database is a protein sequence database compiling the following
You are able to enter the PDB code for most proteins (Swissprot
recognizes them) and get back a short 1-2 page summary of relevant
references, an explanation of its function, and a picture of it.
Within the text files of proteins downloaded from Brookhaven are
references to publications. Most of the magazines have 1-2 paragraph
abstract located on the PubMed server. PubMed is a branch of The National Center for
Information The references within the PDB files look like:
- SWISSPROT Bairoch, A. & Boeckman, B. (1991)
- PIR(1-3) Sidman, K., George, D., Barker, W. * Hunt, L. (1988)
- GenBank translations Benson, D, Lipman, D., & Ostell, J. (1993)
- NRL-3D Pattabiraman N., Lowrey, A., Gaber, B., George,D.G. &
Where the 8 digit code at the end is the only thing that differs in all
- Structural Classification of Proteins
" Nearly all proteins have structural similarities with other proteins
and, in some of these cases, share a common evolutionary origin. The scop
database, created by manual inspection and abetted by a battery of
automated methods, aims to provide a detailed and comprehensive
description of the structural and evolutionary relationships between all
proteins whose structure is known. As such, it provides a broad survey of
all known protein folds, detailed information about the close relatives
of any particular protein, and a framework for future research and
Origami Related Sites
OrigamiThis site makes a
"connection between modular origami and geodesic principles." You
have a structure whose components are in tension and compression.
Molecular Origami referring to the unfolding of proteins. In an actual paper origami structure you can unfold it and tell by the folds exactly how to fold it back up. This page is devoted to doing the same with proteins to learn about how they fold and unfold, a topic that is not yet understood.
Art - An essay about origami as an art and a mathematical science.
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