About Protein Explorer

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Information about, and help for Protein Explorer is available at the
The Help, Index and Glossary is available by clicking the circled green question mark near the top of each control panel, or from the PE Site Map, available on all control panels.

Protein Explorer is Copyright © 2006 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.

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.

Coauthors and Acknowledgements

Protein Explorer's major support is from the Division of Undergraduate Education of the National Science Foundation (Awards 9653427 and 9980909).

PE's Flash Demo movies were authored by Frieda Reichsman and Eric Martz. PE's Script Recorder was designed largely by, and implemented by Timothy Driscoll, who also implemented PE's Undo and History mechanisms. Enrique Castro solved the major problems for compatibility with the Gecko family of browsers (Netscape 7, Mozilla, and Firefox) and kindly documented the fixes in detail. This provided a crucial foundation for Eric Martz to develop full compatibility. Portions of the MSA3D javascript were generously contributed by Paul Stothard.

Paul Pillot made crucial contributions to adapting PE to operate in Internet Explorer by identifying and solving some of the major problems and demonstating that PE could operate reliably within IE. Thanks also to Jean-Philippe Demers who earlier had provided convincing evidence that operation in IE should be possible. Both contributions were initially made as volunteers. Thanks also to the Chime Team at MDL for quickly adapting Chime 2.6SP3 to work effectively with Microsoft's sudden changes in IE 5.5SP2.

Thanks to Philip Bourne, the Protein Data Bank, and the San Diego Supercomputer Center for encouragement, to Helge Weissig and Kenneth Yoshimoto for interfacing with the PDB website, and John Badger for much useful advice and discussion. Thanks to Joel Sussman and Jaime Prilusky for their encouragement and collaborations initiated at the Brookhaven PDB and continuing at the Weizmann Institute of Science. Special thanks to Jaime Prilusky for implementing a search for specified PDB record names, which was a big help in implementing Features of the Molecule.

Thanks to Gale Rhodes, Kurt Giles, Craig Martin, Judith Voet, Frieda Reichsman, Tim Driscoll, Nicholas Keep, Kim Henrick, Diana Ditmore, Pablo Alvarez, Gabriel Pons, Miguel Howard, Byron Rubin, Shigehiro Nagashima, and Karsten Theis for helpful suggestions and expert advice.

Thanks to Diana Ditmore for coding the routines that make the QuickViews Water, Ligand and 2o buttons, the Vine and Cartoon displays, and the Polarity and ACGTU color schemes work more efficiently for large molecules. Thanks to Cris Necocea for expert javascript advice critical to Features of the Molecule and the PE Site Map.

It would not have been possible for me, working alone part-time for a few years, to have created Protein Explorer without the power inherent in MDL Chime. Chime would not have been possible without the power and speed achieved by Roger Sayle in RasMol, and his generosity in putting RasMol's source code into the public domain. Thanks to Tim Maffett of MDLI for keeping nearly all of RasMol's power in Chime, for making Chime such a powerful tool, for implementing many requests that I made, and for crucial guidance. Thanks to Bryan van Vliet, Franklin Adler, Jean Holt, Robert Dickey, and the rest of the Chime team at MDLI for Chime 2, and for much helpful advice. Thanks to Jean Holt for implementing my request for "show pdbheader" in Chime 2.6.

Thanks to Miguel Howard for implementing most of Chime's command script language in Jmol, which although not yet used in PE, provides an open-source route for future development of PE.

Diagnosing the "Script-Disabled Chime in IE" problem, and devising a solution to it in 2002 (search for "broken chime" here), would not have been feasible without the use of virtual machines from VMWare, which continued to be useful in debugging Windows XP Service Pack 2 compatibility issues in late 2004/early 2005.