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multivariate infometric analysis S.r.l.

overview

what is new

hardware requirements

licenses

screenshots

on-line manual

download Golpe 4.5 (Irix -SGI)


GOLPE 4.5



OVERVIEW

GOLPE (Generating Optimal Linear PLS Estimations) is the state of the art chemometric toolbox for 3D QSAR. Designed and implemented by the same people using it in practical scientific work, implements everything it is needed to build, validate and interpret 3D QSAR models.

GOLPE incorporates the FFD GOLPE variables selection method, but GOLPE is much more than just variables selection:
  • PCA and PLS models
  • Cross-validation using LOO, LTO, random groups, etc...
  • Advanced data pretreatment, including zeroing, minimum sd, autoscaling, Block Unscaled Weights, removal of variables with skewed distribution, etc...
  • Grouping of variables using Smart Region Definition.
  • Nearly every kind of plot you can conceive: 2D, 3D and Grid plots, histograms and the revolutionary 2D-3D active plots. Any number of plots can be viewed simultaneously.
  • Imports structures in PDB, GRID kout, SYBYL mol2, Insight car, etc.... Imports SYBYL, GRID and Spartan field data. Also import AMBER ANAL output for COMBINE analysis.
  • Produces output in RGB, PostScript and HPGL formats. Contours can be exported as SYBYL cnt or Insight grd files.
  • Prepared for handling large datasets. Up to 500.000 variables and 100.000 objects. Really fast model building and validation.


WHAT IS NEW

Version 4.5 incorporates many improvements and new features:

new graphics
  • New Grid plots. Data can be represented as symbols, contours and solid or transparent surfaces. Levels can be defined interactively. Full control over the colors of the data and the background.
  • The new Grid plots can import and manipulated molecular structures directly. Support structures in format mol2, pdb, car, kout and cssr. Multiple structures can be imported using drag&drop (imports up to 100 structures in a few seconds).
  • Molecular structures can be presented as wireframe, sticks, ball and stick or CPK models and colored by atom type, by a color selected by the User or by properties.
  • Support of SGI stereo hardware.
  • Output in Inventor format. The output can be pasted right into SGI Showcase and edited interactively or converted to VRML to create interactive graphics which can be incorporated in any WEB for visualizing in Internet or intranets without the use of proprietary tools.
  • Many bug fixes and code speedup.

new tools

  • The molecular fields can be filtered using the proximity of the nodes to a template structure. Regions containing no information or disturbing field values can be easily removed.

new GUI

  • Improved GUI. Thank to the suggestions of many Users GOLPE is now much more intuitive and easy of use.
  • Improved Installation Tools. Your version of GOLPE can be updated to version 4.5 in few seconds. No new keys required.
  • Use of tear-off menus and persistent dialogs to avoid repetitive operations.

Please visit the link to the screenshots and to the on-line manual to see a more detailed description.



HARDWARE REQUIREMENTS

GOLPE 4.5 runs on SGI workstations with MIPS 2 CPU's (MIPS R4000 or higher) and version 6.2 or higher of the IRIX operative system.

Support of MIPS R3000 CPU's and IRIX 5.x has been discontinued.



LICENSES

GOLPE is distributed worldwide by MIA S.r.l. Since CoMFA is a methodology patented by Tripos Inc., GOLPE can be distributed only to TRIPOS customers with a valid license for the SYBYL modules QSAR and Advanced QSAR.

If your position complies with that binding requirement, please click here for downloading Golpe 4.5 (Irix-SGI), unpack the compressed archive file and proceed with the installation following the instructions contained in file "install.pdf".

If you want to know more about the contractual conditions of the GOLPE license you can download a copy of the commercial and academic licenses, either in HTML or in PDF (Acrobat 3.0) format. If you have any doubt, please contact us.


get Acrobat Reader



SCREENSHOOTS

Click on the thumbnail to see a full size image. Due to the high image compression used the quality of the pictures is lower than the real plots.


INTERFACE
Motif GUI GOLPE uses a Motif graphic user interface. All the operations are performed using intuitive graphic controls (menu panes, buttons, slides, etc...). Version 4.5 is integrated into the Silicon Graphics Indigo Magic environment.
Pretreatment dialog Complex operations, like variable pretreatment are performed using an integrated tool in which single operations can be chosen from a palette and applied sequentially to the data.
GOLPE can import a large variety of structure formats. Many structures can be imported at the same time simply dragging the icons from a folder and dropping them into the window.

Structures can be presented as wireframe, sticks, CPK models, etc... . Molecules can be colored by atom type or different colors can be assigned to different structures.
drag and drop


PLOTS
GOLPE produces more than 40 different plots: 2D, 3D, grid plots, etc... They have been carefully designed to highlight the information that you need.

For example, the compounds can be colored by their activity, by their chemical type, etc... They can be represented as numbers, as names or as geometrical objects (points, crosses, cubes, circles, etc...)
2D plot

3D plot

profile
spheres

contours
Grid plots are important to show the results of the analysis on the real space around the molecules.

GOLPE can present those results as solid or transparent surfaces, isocontours or with symbols (crosses, cubes, spheres) which take different sizes according to the values.
levels

surface
Isocontours can be produced with a single mouse click. The level of contour can be modified interactively for positive and negative values.

Contours can also be exported to your favorite molecular modeling software (SYBYL and Insight).


INTERACTIVE PLOTS
clipboard Look to the PLS weight plot on the left of the figure. Can you guess the identity of the variables more directly related with the activity?
Now it is simple!
Surround the area you want to individualize in any 2D plot and those variables will be highlighted in a grid plot.
GOLPE answer the questions you always wanted to ask: why the model predict compound (ihydan) to be more active than (icar)?.

Simply click with the mouse over those two compounds and see the interaction responsible of those differences.
PLS interactive plot