"in silico DNA, RNA, Protein Sequence,
and Structure Analysis:

Theory and Practice"


Friday, 10 January 1997


Morning Lectures

9:30 AM Analysis of Three Dimensional Structure: Voronoi Polygons and Distance Geometry; Three Dimensional Imaging

"From Secondary Structure to Tertiary Structure: Alternative Aesthetics of Moelcular Origami"

As introduced on Thursday in the context of studying secondary structure, modelling can be informed by multiple perspectives. After viewing three dimensional stereo slides of biological macromolecules, we will explore how aesthetic considerations can inform our modelling approaches. In particular, we will use a result from distance geometry (Voronoi polygons and Voronoi polyhedra) to understand the nearest neighbor packing constraints of side chain residues. We will show how these can be modelled with origami paper folding, compass and straight edge drawings, and baking bread as well as with some elegant (and elementary) mathematics. We will also consider how two dimension models help us build three dimensional models.

Bibliography

10:45 AM Break

11:15 AM Analysis of Three Dimensional Structure: Group Theory, Symmetry, Reciprocal Space; Unit Cells; X-ray Crystallography (Dr. Everse)

"3D"

We often hear or read terms like: "solve a structure", "unit cell", "crystals", "molecular replacement", "asymmetric unit", "heavy atom derivative", "phases", etc. What do these terms really mean? What is involved in "solving a structure"? Can anyone "solve a structure"? We will examine the answers to these questions and move through an active dialogue using real world examples.

Bibliography

12:30PM - 2PM Lunch

Afternoon Laboratories

2-3:30 PM Secondary structure prediction of proteins and Software for Three Dimensional Analysis of Protein Structure

SOFTWARE: A demonstration of O (UNIX) viewing/building molecular models, PredictProtein (web), PredictProtein (web) [predicts 3D structure], rasmol (MacOS, Windows, Unix) viewing PDB files

3:30 PM Break

3:45 - 5 PM Continuation of the early afternoon session expanded to include other programs that do similiar things.

SOFTWARE: Antheprot (web), BCM PSSP (web), GOR (web), nnPredict (web), Swiss-Model (web) [predicts 3D structure], MolScript (Unix) [draws ribbon diagrams]

4:30 - 5:00 PM CONCLUDING SESSION


Software:

O

Description: O is a general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build and display macromolecules. O is a graphical display program built on top of a versatile database system. O brings into use several tools, which ease the building of models into electron density, allowing this to be done faster and more correctly. Notably, the autobuild options greatly enhance the speed of building and rebuilding molecular models. O runs on UNIX workstations from Silicon Graphics, Hewlett Packard and Evans & Sutherland.

Written by: T. A. Jones (Uppsala University, Sweden)

For more information: O homepage


RasMol

Description: RasMol is a free program which displays molecular structure. It is available for on PC/Windows (RasWin), MacIntosh (RasMac), unix, and VAX VMS (the latter two via X-windows), and also (through ports by users) for NEXTSTEP. RasMol is a powerful educational tool for showing the structure of DNA, proteins and smaller molecules in beautiful, space-filling, colored, 3-dimensional images.

Written by: Roger A. Sayle (GlaxoWellcome & University of Edinburgh, UK)

For more information: RasMol homepage

MolScript

Description: MolScript is a UNIX program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. Colour, greyscale, shading and depth cueing can be applied to the various graphical objects.

Written by: Per Kraulis (Uppsala University, Sweden)

For more information: MolScript documentation



Webware:



Protein Sequence Analysis at IBCP, France






BCM protein secondary structure prediction






GOR Secondary Structure Prediction





NNPREDICT Protein Secondary Structure Prediction




The PredictProtein server





Swiss-Model An Automated Knowledge-based Protein Modelling Server




Other handy resources:

Bookstores:

  • Academic Press
  • Amazon Books over 1 millions titles availible

    News:

  • CNN
  • New York Times newspaper

    Encyclopedia:

  • Britannica Online


    Bibliography - From Secondary Structure to Tertiary Structure: Alternative Aesthetics of Molecular Origami

    Crippen, G. M. and Havel, T. F. 1988. Distance Geometry and Molecular Conformation, Research Studies Press, Ltd., Somerset, England, pp viii-23.

    Crippen, G. M. 1988. "Voronoi Polyhedra Site Models." Distance Geometry and Molecular Conformation, Research Studies Press, Ltd., Somerset, England, pp 407-414.

    Tsai, Jerry, Gerstein, Mark, and Levitt, Michael. "Using Voronoi polyhedra in the analysis of molecular dynamics simulations of small molecules and proteins in aqueous solution." Stanford University, Department of Structural Biology.

    Thornton, Janet M., Orengo, Christine M., Michie Alex, Miller, Rob, and Jones, David T. "Protein Structure Classification and Threading." Biochemistry and Molecular Biology Department, University College, Gower St., London WC1E 6BT. http://www.biochem.ucl.ac.uk/bsm/

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    Bibliography - 3D

    Phavanantha, Phathana. "Crystallographic Schools in Thailand and Neighbouring Countries." Chulalongkorn University, Bangkok 10330, Thailand.

    Kastner, Margaret E. "Instructional Materials." Department of Chemistry, Bucknell University, Lewisburg, PA 17837.

    Other Suggested Readings (not attached):

    Branden, C. & Tooze, J. 1991. Introduction to Protein Sructure. New York: Garland Publishing, Inc.

    Glusker, J.P., Lewis, M., & Rossi, M. 1994. Crystal Structure Analysis for Chemists and Biologists. New York: VCH Publishers, Inc.

    Rhodes, G. 1993. Crystallography Made Crystal Clear. San Diego: Academic Press, Inc.

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    Last modified: Thur Jan 2 19:01:47 1997