from the Stephen White laboratory at UC Irvine

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 problem anymore.

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 values.
• 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, e.g.:
      proteinName -------YLGGAVALIVGVAFWLLY----------ALAPLAIIPV...    (TM segments)
  or
      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 3-d appearance.
• 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 mode.
• 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 for saving.
• 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 Wimley-White Scales.
• 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 errors.
• 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 selection.
• 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:	Has become:
  rec_num	record_number
  db_type	db_type
  protein_name	protein_name
  file_name	file_name
  entry_date	entry_date
  refm_num	refman_number
  author	author
  remarks	remarks
  pir_version	pir_number
  pir_num	Swiss_Prot_entry
  pdb_num	Swiss_Prot_number
  pir_title	Swiss_Prot_gene
  pdb_title	Swiss_Prot_name
  Nterm	PDB_title
  numtmsegs	PDB_Identifier
  tmseg_range	N_terminal
  seq	number_tmsegs
  	tm_segments
  	sequence

• The "Mark User TM Segments" tool has become the "Mark/Measure Segments", and now provides a transfer free energy value for user-marked segments.
• 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 and improved.
• 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 related functionalities.
• 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 "Visible" toggle.
• 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 printed.
• 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 modified sequences.
• Comments can now be added for retention with each plot stored in the buffer.
• 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 their states.

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 Locate introduced.
• 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 structure.

Version 1.0 - 12 February 2000

• Membrane Protein Explorer (MPEx) released for public use.

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