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MOLECULAR MODELING
The three dimensional crystal and NMR structures of biological molecules can be viewed on the internet using the following programs. If you try to open a file containing the structural coordinates of a molecule your computer will ask you to "configure a viewer". You need to tell the computer which program you wish to use to view the molecule.
The netscape plug-in program Protein Explorer is a program similar to Chimes, and runs on top of Chimes 2.0. Protien Explorer allows you to create ribbon models of molecules for simple analysis of structures. Protien Explorer will also allow you to highlight specific amino acids and to identify contact points between different molecules. Once you load Chimes 2.0 into your plug-in folder on your computer anytime you open a ".pdb" file Protein Explorer will be activated.
For more technical analysis of a structure, including the measurement of distances and bond angles, the program WebMol is recommended. This is a JAVA based program, so your computer will need to be able to run JAVA for this program to work.
STRUCTURAL DATABASES
The first step is to find the structure of a molecule that you wish to examine. Below are links to three sites containing structures. Each of these files will contain the three dimensional coordinates for each atom in that molecule.
Molecules R Us (http://molbio.info.nih.gov/cgi-bin/pdb) A searchable database at the National Institute of Health, with protein and DNA 3D structures in PDB format. Enter the common name of the protein or molecule that you wish to search for.
Brookhaven Protein Database (http://www.rcsb.org) 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.
Library of 3-D Molecular Structures (http://www.nyu.edu/pages/mathmol/library/life/) This is an excellent educational site that contains PDB models of simple biological molecules: lipids, amino acids, carbohydrates and nucleotides. Select the box "PDB" below an image to view it with Chimes.
PROTEIN EXPLORER
Enter the
Protein Explorer site and either enter the name of the .pdb file you wish to open, or download the .pdb file directly. A few examples files are provided.
To move the structure use the left button on your mouse.
To zoom in our out hold down the shift key and the left button. Pushing the mouse away from you will make the structure smaller. Pulling the mouse towards you will make the structure larger.
By pressing the right mouse you will be given more opitons.
- Display
gives several options for displaying the structure as a wire frame or stick model. If you are looking at a protein you can make a ribbon diagram of the backbone of the protein. Spacefill generates a model showing van der Waal radii.
- Options allows you to turn on or off hydrogen atoms, H-bonds and disulfide bonds.
- Color allows you to change the color of the atoms.
- CPK
colors each atom a different color; O=blue, N=red, etc.
- Shapely colors each amino acid a different color; His=blue, etc.
- Chain colors each subunit a different color.
- Structure colors alpha-helicies red, beta-sheets gold, random structures white.
- Polarity colors amino acids as hydrophobic (gray) or hydrophilic (purple)
Under the heading Explore More! you have the option to selectively display and color individual chains in a structure. Selections include cartoons, ribbons, ball and stick and surfaces.
Under the heading Seq3D you can selectively display individual amino acid and nucleotide residues by selecting the individual amino acids at the bottom of the pop-up window.
WEBMOL
(To use JAVA© at this website, you'll need to be running Netscape 3.0+ or MS Internet Explorer 3.0+ on a Macintosh or Windows 95 computer) For more help, see the tools section.
WebMol allows one to make measurements of atomic distances and angles and to analyze NMR data from protein structures. It can be accessed at the following address and runs as a JAVA application on your computer. http://www.cmpharm.ucsf.edu/cgi-bin/webmol.pl
Use one of the sites above to identify the code for the structure that you wish to observe. For example the structural coordinates of insulin "9ins". Enter this code into the box in the lower left hand corner of the WebMol viewer and hit "enter".
To move the structure use the left button on your mouse.
To zoom in our out hold down the right button. Pushing the mouse away from you will make the structure larger. Pulling the mouse towards you will make the structrue smaller.
The number and one letter code of the amino acid or nucleotide that your mouse is pointing to will be displayed in the upper right corner.
More options are available through the buttons to the right and below the screen.
- Turning on the option Labels will attach labels to each amino acid or nucleotide.
- The three boxes in the upper right corner will allow you to change the colors used, which atoms are displayed and will generate surfaces (lots of memory required).
- The Select button brings up a window which allows you to choose which amino acids you wish to view. It can be reset by pushing the button "ResetSlab".
- The Focus button allows you to select a single atom and only view other atoms within a set radius. It can be reset by pushing the button ResetSlab.
- Under the box Msure (Measure) you have several options.
- Dist
allows you to measure atomic distances. Click your mouse on the two atoms you wish to measure.
- Angle will measure an angle between three consecutive atoms.
- Dihed will measure the dihedral angle between four consecutive atoms.
- DMat generates a 2-D NMR profile of your structure. You can view both the model and the profile simultaneously and observe the distances between atoms.
- Rama generates a Ramachandran plot of the protein.
- Center allows you to choose a new center of rotation for the structure.
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