HOW TO SEARCH AND VIEW PROTEIN STRUCTURES


Several thousand 3-D structures are directly available for public use from the Brookhaven Protein Data Bank. In addition the Molecules R US Page at the National Institute of Health and the NRL 3-D Database at the Genome Data Bank provide access to PDB files. Depending upon your needs it is worthwhile to become familiar with each of these sites. In addition, the amino acid sequence from an even larger number of proteins is available from several sites.


Brookhaven Protein Data Bank

The Brookhaven Data Bank will contain the most recent entries of all protein structural data. Proteins can easily be searched by using Brookhaven's PDB Gopher. When the box appears type in any key word. If a match appears, select the protein of your choice. Three files will appear: *.biblio, *.full, and *.gif. The first file will only give the information found in the header, it will not give coordinate data, the *.full file gives all data and is needed if you wish to manipulate structures from your own terminal. The *.gif file will contain a single image of the molecule. Remember that many cases several structures will be found for the same keyword. As an example try typing in pepsin after clicking here Next click on one of the many structures that show up on screen. Take a look at each of the files (*.biblio, *.full, *.gif) that are available from Brookhaven.

For more information about the Brookhaven Protein Data Base connect to their home directory which contains FTP access to recent PDB Newsletter. A searchable index by key words can be used to search the Newsletter. Click here to connect to the Brookhaven PDB Gopher


NRL-3D Database

The NRL Database is a is a sequence--structure database derived from the 3 dimensional structure of proteins deposited with the Brookhaven National Laboratory's Protein Data Bank. It does not contain the full listing of coordinates. As an example of what a sample file looks like click here . The NRL Database allows one to perform a Boolean Search. For further instructions connect directly to NRL here .


The National Institute of Health

The NIH Molecules R US Home Page allows output requests in one of three ways.

1) you can download the full file and view the structure with a your own viewer(choose PDB Viewer),

2) you can view the text of the PDB file (choose text)

3)you can view on screen interactively any of the PDB structures. These images can be viewed as either, line-drawing, ball and stick, space filled or ribbons structures. In addition you can input x,y,z rotations for the protein allowing for different views of the molecule. This can be performed on-line without have to download any data. For more instructions connect directly to the Molecules R US page here


To Retrieve and View PDB Structures

If you would like to be able to manipulate and do limited calculation on your PDB file you must retrieve the *.full file from the PDB database. If your present terminal does not have a viewer, several excellent public domain packages are available.

Visit the MathMol Software page here