Award: "Protein Explorer has revolutionized the teaching of biology at a molecular level."

Protein Explorer en español ¡Nueva versión 2.25! Compatible con Microsoft Internet Explorer. PE en Français

proteinexplorer.org
FrontDoor to Protein Explorer
Works in Netscape 7 or 4.8, Mozilla, FireFox, and Internet Explorer.
Copyright © 2005 by Eric Martz    
Bookmark this page. Bookmarking subsequent pages in this site may not work!

			< (Reload page to re-start.) The images at left are animated GIF's prepared with Protein Explorer. Tutorials dedicated to DNA Structure, Hemoglobin, Antibody, Lipid Bilayers and Channels (all downloadable): go to MolviZ.Org, which also has templates for building your own Chime-based websites. World Index of Molecular Visualization Resources, MolVisIndex.Org. linux: Protein Explorer can work well in linux or other unix platforms.
Evolutionarily conserved patches revealed with ConSurf & MSA3D.	Morphs: Rotatable Animations: EF Hand binding calcium	Animated GIF created with PE (morph of lac repressor binding DNA). Shows in Powerpoint without Chime.

 

Protein Explorer Copyright © 1998-2005 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. Co-Authors and Acknowledgements. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the US National Science Foundation.

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.

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.

If you are offered PE version 2.0 or 1.0, select version 2.0!
• Browse PE's Atlas of Macromolecules.
• PDB Lite is a search interface designed for nonspecialists, students and educators. Other search interfaces and resources with built-in links to Protein Explorer:
• SearchFields is an advanced interface offered by the Protein Data Bank/RCSB (www.pdb.org).
• OCA is an advanced PDB searcher at the Weizmann Institute with some capabilities not found in the RCSB search interfaces.
• Specific Oligomers: The PDB file for your molecule may contain only part of the actual molecule. For example 1HHO contains only half of the hemoglobin tetramer. Or it may contain multiple copies when you only want one. After you see the molecule in Protein Explorer, use the PE Site Map link, then External Resources, to access EBI's Probable Quaternary Structures, where you can usually get a single whole molecule.
• No Empirical Structure? Less than 10% of the protein chains coded by most genomes have empirically determined structures. If no 3D structure has been published for your molecule, consider Homology Modeling.
  These don't have direct links to PE -- use them to get the PDB code, then enter it in the slot above.
• PDB at a Glance is a convenient browsable list of molecules, arranged in categories like enzymes, membrane-associated proteins, nucleic acids, etc. etc. Use it to get the PDB code to enter in the slot above.
• Molecules R Us is another user-friendly search interface.
• Micromolecules, lipid bilayers, and other sources of PDB files are indexed at the World Index of Molecular Visualization Resources -- molvisindex.org.

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:

• Simply drag a hyperlink from an existing document (e.g. the Atlas of Macromolecules) into free Netscape Composer. Here are detailed instructions.
• The simplest format for a hyperlink, for example for PDB ID code 1d66, is
  http://molvis.sdsc.edu/protexpl/pe.htm?id=1d66&
  PE automatically gets the PDB file matching the prespecified PDB ID code from the Protein Data Bank server. For two molecules side by side, for example calcium:calmodulin with and without bound peptide:
  http://molvis.sdsc.edu/protexpl/pe.htm?id=1osa&id2=2bbm&
• You can prespecify any PDB file readable from a server. Here are more examples of links to molecules from diverse servers around the world.
• Complete and detailed rules are in the following documents, should you need them.
  • How to make hyperlinks that prespecify molecules
  • Constructing Hyperlinks to PE

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.

To display downloaded PDB files in PE, first start PE "Empty", and PE will start at its "Different Molecule"/"Load Molecule" control panel. There you can use a Browse button to locate and load saved PDB files from your hard disk. PE's "Load Molecules" control panel remembers the last ten files you have loaded and offers to recall them from a pick list. Also, you can make an HTML page containing hyperlinks to your favorite molecules.

"Empty" PE