"Protein Explorer has revolutionized the teaching of biology at a molecular level."
Protein Explorer
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¡Nueva versión 2.25!
Compatible con Microsoft Internet Explorer.
FrontDoor to Protein Explorer

Works in Internet Explorer or Netscape 4.
Copyright © 2003 by Eric Martz    
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    What Is Protein Explorer?  
    Beginners click here:

    Can't get PE to work? Here is Troubleshooting help!
More Quick-Start Molecules

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Larger, slow for modem:

Atlas of Macromolecules

Find Any Molecule
Open optimal (large) windows for new sessions.
About Protein Explorer
< (Reload page to re-start.) The images at left are animated GIF's prepared with Protein Explorer.

Protein Explorer can work well in linux or other unix platforms. Besides Protein Explorer, Other Chime-based Resources include tutorials on DNA, Hemoglobin, Antibody, templates for building your own Chime-based websites, the World Index of Molecular Visualization Resources, and more.

patches revealed
with ConSurf & MSA3D.
EF Hand
binding calcium
(a morph)
Animated GIF
created with PE
(morph of enzyme
binding inhibitor).

Protein Explorer Copyright © 1998-2003 by Eric Martz. Protein Explorer is offered as unsupported freeware. All use is at the risk of the user. No warranty whatsoever is made or implied. This version is free for all users, but downloaded copies or derivatives thereof may not be publically redistributed on CD's, served from publically-accessible websites, or publically redistributed by other means without permission. Permission is given to link to Protein Explorer freely from other websites, provided no fee is charged for access. Permission is given to distribute Protein Explorer locally to students within a class or educational institution, from a nonpublic intranet server, or via CD, provided no fee is charged. Supported by the Division of Undergraduate Education of the National Science Foundation, and the University of Massachusetts. Acknowledgements.

    PDB ID Codes & Files
One Molecule: To see a molecule in Protein Explorer (PE), you must first choose an atomic coordinate file (often called a PDB file) that contains the 3D structure of the molecule. (Protein Explorer cannot calculate the 3D structure of a protein from the amino acid sequence -- see Nature of 3D Structure Data.) Each PDB file has a unique 4-character identification code. Examples: 2HHD (hemoglobin), 1BL8 (potassium channel). If you don't know the PDB ID code you want, see below to find it. After you find the PDB code you want, enter it in the slot above.

Two Molecules: If you want to compare two PDB files ("molecules") side by side, enter two PDB ID codes in the slots below, and click the button.

URL of Molecule: If you know the URL to an atomic coordinate file on a server, paste it below and click Go.
    Two test examples (copy and paste into slot):
   (lipid bilayer with gramicidin channel)
   (NaCl crystal)

    How To Find Molecules
Published macromolecular structures are archived at the Protein Data Bank (PDB). Search for the molecule you want, and then click on the Protein Explorer link built into the search result page. Or, notice the PDB code, and enter it in the slot above.

    Hyperlinks that Prespecify Molecules
You can create web pages containing hyperlinks that prespecify molecules to be displayed in Protein Explorer or Comparator. The PDB files can come from the Protein Data Bank or any other server, or your local hard disk. Examples:

    Downloaded PDB Files
You can download PDB files to keep on your computer's local disk. The most reliable way for novices to download PDB files is by using PDB Lite.

When running "bare" PE, you can use the Browse button (on the "Different Molecule"/"Load Molecule" page) to locate and load saved PDB files from your hard disk. "Bare" PE remembers the last ten files you have loaded at its "Load Molecules" page, and offers to recall them from a pick list. Or you can make an HTML page containing hyperlinks to your favorite molecules.

    "Bare" PE

If you know the PDB identification code(s), or have the PDB files downloaded and saved on your local hard disk, or you have loaded the molecules of interest in a recent session with PE, you can tell PE what molecule(s) to display after you have entered either the Here are instructions for inserting hyperlinks to bare PE or Comparator into your html web pages, and here is a list of all documents concerning Constructing Hyperlinks to PE.  

Click the above visitor count to see breakdown by browsers, operating systems, etc.
Visiting rates, counts of sessions and downloads are also available.