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Copyright © 2003 by Eric Martz    
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			< (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.
Evolutionarily conserved patches revealed with ConSurf & MSA3D.	Animations: 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.

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.
• The PDB file for your molecule may contain only part of it. 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 Molecule Information link, Mol Info, to get a single whole molecule, or just one chain.
• Align 3D protein structures and display the aligned set in PE at the Combinatorial Extension site of Shindyalov and Bourne (San Diego, USA). For example, here's 1atp aligned with 1cmk. (This server does only a pair of chains, and hetero atoms are not retained. For more control with alignments, use DeepView).
• Evolutionarily conserved (or variable) patches in a protein chain are identified automatically by ConSurf, then displayed in Protein Explorer.
• 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.

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