Information about, and help for Protein Explorer is available at the
Help, Index and Glossary
is available by clicking the circled green question mark
near the top of each
or from the
PE Site Map,
available on all
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.
Protein Explorer's major support is from
the Division of Undergraduate Education of the
National Science Foundation
(Awards 9653427 and
PE's Flash Demo movies were authored by
and Eric Martz.
Recorder was designed largely by, and implemented by
Timothy Driscoll, who also implemented PE's
Castro solved the major problems for compatibility with the
Gecko family of browsers
Mozilla, and Firefox) and kindly documented the fixes in detail. This provided
a crucial foundation for Eric Martz to develop full compatibility.
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
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.
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
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.
"Script-Disabled Chime in IE" problem, and devising a
solution to it in 2002 (search for "broken chime"
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.