Origami & Protein Related Links

Getting data

  • 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 fees."

  • ExPASy - Expert Protein Analysis System.
    This is a molecular biology server 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 a two dimensional picture of an protein that is colored and shaded to appear 3D. The 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 Molecular Origami.

  • 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 Structure Center.
    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 through x-ray crystallography or 'NMR interproton distance restraints'
    Much of the PDB's data coordinates have been obtained using a program called X-PLOR that was written by Axel Brünger.

    Downloads from other sites

  • Download RasMol is a program written by Roger Sayle of Glaxo Wellcome.
    The RasMol Users Manual is located online.
  • Chime 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.

    Protein Info

  • OWL database
    The OWL database is a protein sequence database compiling the following source databases:
    1. SWISSPROT Bairoch, A. & Boeckman, B. (1991)
    2. PIR(1-3) Sidman, K., George, D., Barker, W. * Hunt, L. (1988)
    3. GenBank translations Benson, D, Lipman, D., & Ostell, J. (1993)
    4. NRL-3D Pattabiraman N., Lowrey, A., Gaber, B., George,D.G. & Barker,W.C. (1989)
    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.
  • PubMed 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 Biotechnology Information The references within the PDB files look like:
    Where the 8 digit code at the end is the only thing that differs in all the references.

  • SCOP - 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 classification."

    Origami Related Sites

    Geodesics and 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.

    Origami Art - An essay about origami as an art and a mathematical science.

    Related Sites

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