Contents

1. Introduction to Protein Analysis
2. Obtain a sequence of interest.
3. Identify ORF's and translate into protein
4. Identify Similar Proteins from the Databases
5. Align your sequence vs similar sequences and look for Gene Families
6. Determine the putative function of your protein
7. Determine the putative structure of your protein
8. Protein Structure Visualization Tools
9. Other Interesting Things You Can Do With Proteins

VIII. Protein Structure Visualization Tools

1. RasMol
   http://www.umass.edu/microbio/rasmol/rasquick.htm
   
   • Developed by Roger Sayle at University of Edinburgh
     
   • One of the first free viewers available, still a standard
     
   • Free stand alone viewer, available for PC, Mac, UNIX, VAX, NextStep
     
   • Tutorials available (http://www.umass.edu/microbio/rasmol/rastut.htm)
     
2. CHIME
   http://www.umass.edu/microbio/chime/index.html
   
   • Very similar to RasMol, but displays image in a web page.
     
   • CHIME is a browser plugin
     
   • Useful for teaching
     
   • Instructions for using and creating CHIME files are available from this site
     
3. MAGE
   http://kinemage.biochem.duke.edu/default.html
   
   • Developed by David Richardson at Duke University
     
   • Free stand alone viewer, designed for viewing "kinemages" - kinetic images
     
   • Available for all platforms (PC, Mac, UNIX, LINUX)
     
   • Often used for teaching purposes
     
   • Tutorials available (http://www.nyu.edu/pages/mathmol/modules/tutorials/tutorials.html )
     
4. Cn3D
   http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.html
   
   • Developed by NCBI
     
   • Free stand alone viewer, available for PC, Mac and UNIX
     
   • Tutorial available (http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dtut.html )
     
5. WebMol - Java PDB viewer of atomic coordinates
   http://www.embl-heidelberg.de/cgi/viewer.pl
   http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl (US Mirror)
   
   • Written in Java and can be used as an applet or downloaded as a stand-alone application.
     
   • The programming API is also available for download.
     
   • This program is loaded with viewing and rotation options, however it is very slow when viewing large files or complex options
     
6. Molecules R US - Retrieve atomic coordinates at the NIH (Slow!)
   http://molbio.info.nih.gov/cgi-bin/pdb
   
   • Search PDB by keyword.
     
   • Once a molecule is selected for viewing, you may choose from the following format options:
     
   • Raw Data (Text) - the original PDB raw data file
     
   • PDB Viewer* - Interactive structure (requires a program which can read PDB files, e.g. RasMol)
     
   • Mage Viewer* - Interactive structure (requires the program Mage)
     
   • Motifs (RasMol)* - Interactive structure with Protein Motifs patterns highlighted (requires RasMol 2.6)
     
   • H-Bond Map (Mage)* - 2D "hydrogen bond map" of a protein structure(requires the program Mage)
     
   • Line Drawing (GIF) - Image generated on the server by RasMol or Raster3d
     
   • Ball and Stick (GIF) - Image generated on the server by RasMol or Raster3d
     
   • Space Filling (GIF) - Image generated on the server by RasMol or Raster3d
     
   • Ribbons (GIF) - Image generated on the server by RasMol or Raster3d
     
   • Stride 2D Analysis (Text) - output of the secondary structure analysis program Stride
     
   • Torsions (Text) - Returns the backbone torsion angles associated with a protein structure
     
   • Backbone (JAVA) - Uses the PDB3D Java APPLET to render alpha carbon traces of protein structures.
     
   • 3D Line (JAVA) - Uses the WebMol Java APPLET
     
   • 3D Line (VRML) - Interactive 3D line drawing of the structure in VRML format.