Version 3.3.1 January 2024
MPEx now uses jDeploy (https://www.jdeploy.com) for downloading/deployment.
Apple stopped providing a package that allowed the "About" menu dropdown, but that functionality has
appeared in more recent versions of the Java Runtime Environment (JRE). MPEx now requires at least
Java version 11. The new deployment strategy should install the necessary JRE version during MPEx installation.
UCI firewall has blocked our database port, and the MPEx menu bar MPExFile -> Read File -> From MPtopo Database
selection is not currently working. We hope to re-enable this feature soon.
Version 3.2.15 February 2016
Multiple FASTA sequences within a single file weren't being parsed correctly if they contained empty lines.
Version 3.2.14 May 2015
Oracle doesn't seem to be including the com.apple.eawt components of the Java runtime library, rt.jar, in
jre downloads for Windows platforms. MPEx uses these
on OS X platforms, and makes a check to only use them there, but Java doesn't allow conditional compilation,
and when Java runtime environment tries to import these on a Windows platform, they aren't there, giving a
fatal error. The rt.jar library with these components is now packaged with MPEx so we shouldn't have this
Version 3.2.11 January 2014
Fixed another problem with translocon tm analysis predictions for conditions where a predicted segment
might fall at the very beginning of a sequence (thanks again to Johan Nordholm).
All sliders are now Swing JSliders. Took a little work because JSlider doesn't directly deal with Double
Tried to clean up resizing main frame to accommodate MPEx's preferred size, if necessary.
Version 3.2.10 - January 2014
Fixed a problem with translocon tm analysis predictions for conditions where a predicted segment
might fall at the very beginning or very end of a sequence, as in http://www.uniprot.org/uniprot/P03470.fasta
(thanks to Johan Nordholm for finding this problem).
Version 3.2.9 - December 2013
Batch processing of FASTA files updated to allow multiple FASTA sequences within a single file.
Fixed "off by one" error in handling mptopo protein sequences.
Parameter panels now have scroll bars, if needed.
Version 3.2.8 - 2013
Adapted mptopo interface to use new mptopo database.
Version 3.2 - December 2009
Batch processing of FASTA format sequence files is now available for
Hydropathy and Translocon Transmembrane analysis modes. Select
the "Batch Processing" tab.
MPEx is now able to write files with predicted transmembrane sequences
or predicted loop sequences for Hydropathy and Translocon TM analyses,
proteinName -------YLGGAVALIVGVAFWLLY----------ALAPLAIIPV... (TM segments)
proteinName MDAVATA-------------------RSLDGSPhQS----------... (loop segments)
Users may now define hydropathy scales for Hydropathy Analysis.
In Hydropathy Analysis, the neutral residues plot legend reflects
only neutralized residues, not all possible neutralized residues as
in previous versions of MPEx.
In Translocon TM Analysis, free energy calculations for known TM segments has been corrected.
Totalizer now allows use of the Translocon TM scale.
In Totalizer, displaying the helical wheel from either the
N-terminus or C-terminus perspective is now possible.
Rotation of the wheel around the helix center axis and control
of wheel radius are now available. Added some shading to suggest
For Mac OS X: Moved menu bar items to Mac's application menu bar.
Updated and cleaned up internal library usage for 30% overall
program size reduction.
Version 3.1 - April 2009
Added new analysis mode: Translocon Transmembrane.
Moved Totalizer from separate window to tabbed analysis
Updated saving data to tab-delimited text file: Because
of the number of data sets the new translocon TM analysis
mode is capable of generating, it made sense to allow a
user to select an arbitrary subset of the data sets available
Disabled PIR database access.
The MPExView drop-down menu is gone. "View" menus typically
allow a user to modify the appearance of some aspect of a tool,
and MPExView was displaying data windows, so they've been moved
to the MPExWindow drop-down menu. The MPExWindow menu provides
access to windows that don't have another direct means of accessing
them, and is limited to Results, Sequence, Log, and
Analysis mode selection tabs are now differentiated to indicate
different catagories of analysis. Analysis modes that generate
data sets that can be saved to a data buffer (and displayed in
Data Buffer Overlays) appear in a bold font. These
modes will also display a check mark to indicate there is a valid
data set for that particular mode. The validity of a data set
may change when, e.g., a sequence residue is changed, or restored
from a change. Selection tabs for other analysis modes appear
in a plain font.
The end group values for the hydrophobicity scales used in
Totalizer have been revised. Thanks go to Paulo Almeida,
Associate Professor, Dept. Chemistry and Biochemistry,
University of North Carolina Wilmington, for catching these
MPEx is no longer available as a Java Applet, but uses
Java Web Start technology instead. Web Start is part of all
contemporary Java runtime environments.
Version 3.0 - August 2005
Moved from awt to Swing as the main GUI interface library.
Using Swing facilitated the move to using tabs in the plotting
region as a means of selecting the analysis or data display mode.
This means that a new window doesn't have to open for different
functionality, e.g., Buffer Overlays. Selecting a tab reconfigures
the plotting region and the control panel as appropriate for the
Added β-barrel analysis mode.
Displaying the hydrophobic moment plot is now accessed from the
hydropathy analysis control panel rather than the MPExView menu.
The lengh of the moment vector in the Helical Wheel window is now
directly proportional to the hydrophobic moment value (previously
it was segmented into one of four possible lengths).
Version 2.2 - 19 September 2003
Added the ability to save a work session, retaining all state
information, to a file and restore from a saved session (.mpx) file.
Hydrophobic moment plots are now available, controlled by the new
MPExView pull-down menu. The hydrophobic moment plot data is also
available by using the "Save Data as tab delimited text file" under
the MPExFile pull-down menu.
Access to the Swiss-Prot protein database is now available. Use
MPExFile/Read File/from SwissProt Database.
The MPtopo Querier tool is simpler, searches on more fields, and works
far better than the previous version.
The MPtopo database itself has also been structurally modified to
work more effectively with Version 2.2. Warning: Querier in Version
2.1 and earlier releases will not work properly with this new version
of the MPtopo database:
|The old table:
The "Mark User TM Segments" tool has become the "Mark/Measure
Segments", and now provides a transfer free energy value for
Main control panel reorganized to better reflect functionally
related controls. Summary panel of current state included.
The Totalizer tool now has a panel summarizing its results,
and the interaction between the controls has been repaired
The Helical Wheel now has a panel with a summary of pertinent data.
"Protein Name" field changed to "Sequence Description" and moved
to graph area, along with field indicating from which buffer
currently displayed graph was loaded. These values now print
when printing the graph area.
Printing is improved. Text files are formatted to wrap lines at 60
characters/line. This is generally the default line for
representing amino acid sequences, so it should be easier to
visually verify consistency.
Printing of graphics has also been improved - images should scale
to fit regardless of page orientation, although there still may
be some minor clipping of the outer edges. This will be corrected
when we make the leap to Java Swing.
Version 2.1 - 1 March 2003
Main control panel reorganized to improve aesthetics and reflect
Buffer controls on main window have changed. "Load", "Delete",
and "Comment" now have popup menus associated with them for choice
of specific buffers.
Controls on the Overlay window have changed. Except for "Print",
each buffer label now has a popup menu with available operations.
Overlay window operations Remove and Restore are replaced with
Ability to reorder buffer graph layers in Overlay window added.
Graphing region cursor now positioned automatically to first (or
last, for residue window resizing) residue that allows values in
control panel window. Done for new proteins and when residue
window is resized
The three-letter symbols on the "Mark Residues" window have been
reordered alphabetically. The Helical Wheel window now lists
the total hydrophic moment, subsequence hydrophobic moment, total
free energy, and subsequence free energy.
In the Helical Wheel window, if "Draw 18" is selected, the 18
residues drawn in the window are highlighted in the "Sequence"
text area as these 18 are shifted left or right.
The cursor position indicator window is now above the graphing
region instead of below it.
Extended the color coding of writable and non-writable text
fields - white is editable.
Disabled many controls until there a valid sequence is in the workplace.
Added an MPEx label to the main window that responds intelligently to
different window sizes and has more aesthetic appeal.
All deprecated Java code has been replaced.
Version 2.04 - 13 November 2002
MPtopo querier was lost in version 2. This error has been
corrected, which permits keyword searchs of MPtopo from within MPEx.
Version 2.03 - 25 October 2002
Corrected a consistency error in Totalizer operation. Improved
loading of applet under Java Plug-in 1.4.
Version 2.02 - 3 October 2002
Corrected Totalizer default hydrophobicity scale to be "interfacial".
Version 2.01 - 30 September 2002
Corrected an error in Totalizer that caused partitioning free energies
to be computed incorrectly.
Version 2.0 - 23 September 2002
The java code was extensively revised to simplify future changes.
Calculate button was removed. All calculations are now performed
automatically every time a change is made in the sequence properties.
The effect of making salt-bridges can now be examined. Setting
salt-bridges invokes the hydrophobicity parameters discussed in
Jayasinghe et al. (2001), J. Mol. Biol. 312: 927-934.
Management of plots stored in the buffers was improved significantly.
Control of buffers was made a prominent feature by placing the
controls within the main MPEx window. The buffer overlays can now be
The slider for moving the cursor along the plot was removed. The
cursor can be repositioned by dragging with the mouse or by using
the left/right arrow keys.
The protein can be renamed, which is useful when working with
Comments can now be added for retention with each plot stored in
The Results window keeps track of all changes made in the sequence
properties, such as salt bridges and changed residues.
The Helical Wheel feature of Totalizer has been improved.
The legends in the plot region were improved, including a change
in color scheme for Marked Residues. The Marked Residue legend
now provides more information on the classes of residues and
Version 1.50 - May 2001
The changes below yield single-helix prediction accuracies of 99%
using the MPtopo 3D_helix database.
A new algorithm for determining the positions of TM helices using
Default CONH value in MPEx reset to 0.0 kcal/mol.
Version 1.42 - November 2000
Modified Totalizer to allow computation of sequence hydrophobicity
values without specifying endgroups. This is convenient for computing
the hydrophobicity of a subsequence within a longer sequence.
Version 1.41 - November 2000
Reset the default CONH value in MPEx to +0.1 kcal/mol. This reflects
our latest assessment of the optimal value, based upon TM helix
prediction using the 3D_helix dataset of the MPtopo database.
Version 1.4 - September 2000
Modified MPEx so that even-numbered window lengths can be used
in the Scan Mode.
Modified MPEx such that in the Scan Mode the Results Window
displays the favorable TM regions correctly.
Modified the Totalizer module input panel in order to clarify
that calculations of free energies related to helix
formation apply only to the interfacial hydrophobicity scale.
Fixed the Totalizer module such that the transfer free energy
calculation correctly accounts for endgroup modifications.
Version 1.3 - July 2000
Modified MPEx such that the starting residue number can be set
to any user-selected value.
Added the ability to save hydropathy plots in the workplace
to a buffer.
Added the ability to generate overlay plots of buffer contents.
Version 1.2 - June 2000
Modified MPEx such that the PIR entry numbers appear in the protein
name text field when a protein is read from the PIR database.
Modified MPEx such that the protein name, as it appears in the
protein name text field, is printed along with the graph.
Removed the hydrophobicity value and hydrophobicity scale
information contained in the helical wheel display window.
Version 1.1 - May 2000
Default hydrophobicity scale changed to the 'Octanol' scale.
Default CONH value set to +0.15 kcal/mol.
Fixed a bug in the MPtopo Reader window that caused improper
drawing of window contents.
Renamed the MPtopo Reader database subset selectors to 3D_helix,
1D_helix, and 3D_other (from 3D, 1D, and Other, respectively).
Modified the Totalizer module to enable water-to-bilayer transfer
free energy calculations for peptides with helical secondary
Version 1.0 - 12 February 2000
Membrane Protein Explorer (MPEx) released for public use.