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Shape-based alignment of molecules PDF Print
Written by Sarkis Dallakian   

I was looking for an open source project that would do small molecule alignment and I finally found it. There are many publications out there that describe different algorithms for small molecule alignment, but I couldn't find any that I can try myself. I was very excited to read release announcement for Piramid that does exactly what I was looking for. Below are my initial results.

3D SFD CID_3107 3D SFD CID_9950643
Molecules from the first raw shown together. CID_3107 is highlighted. The same molecules after aligning them.

Update: The URL and the name of this tool has been changed since I wrote this post. This tools is now called Shape-itâ„¢ and it's avialabe from http://silicos-it.com/software/software.html.

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Last Updated on Friday, 31 January 2014 14:51
List of Changes in PyRx Version 0.7 PDF Print
Written by Sarkis Dallakian   

The following are list of changes in PyRx version 0.7.

Version 0.7 - 9 Jun 2010

  • Fixed Make Macromolecule on Mac.
  • Fixed error message that showed up upon completion of remote jobs.
  • Fixed startup problems for Windows. Read PyRx wont start for more info.

Version 0.6 - 21 May 2010

[56]: Created Preferences page for Ligand Preparation. Users can now inactivate all torsions or limit the number of torsions using Edit -> Preferences widget shown below. These options will be in effect when using AutoDock -> Make ligand menu in Molecules panel, and also when doing Convert Selected or All to AutoDock Ligand (pdbqt) using Open Babel widget.


[54]: Fixed MacOS X Drawing bug.

[52]: Analyze Results widget can now be sorted by (left) clicking on table header.

[47]: Added AutoDock Vina interface and included Vina 1.1.1 binaries in the installers. The new Vina Wizard, as shown below, is now the default docking wizard. Also, merged Select Ligand and Select Macromolcule page into a single Select Molecules page.


[44]: Switched from TextCtrl to RichTextCtrl to handle large files. It would be possible, in the future, to add other functions to the toolbar as shown in wxRichTextCtrl overview.

[43]: Fixed problems with axes.set_xlim in Table Plotting widget.

[42]: Added try/expect in showHistogram to log possible errors with clustering. See also Clustering bug.

[41]: Moved from AutoDock 4 to AutoDock 4.2 parameters. This suppresses "WARNING: Using autodock4.0 unbound extended model in autodock4.2!" in the log file. Thanks to Adam Lesser for reporting this.

[40]: Bug fix - fixed problem with Flexible Residues. Now it converts original file into pdbqt before passing it to AD4FlexibleReceptorPreparation. See also: Flexible ligands Bug.

[39]: Bug fix - if there is a problem with writing to PyRx folder, it will now use a temporary folder and inform user about that. See also: PyRx fails to run on OSX.

[37]: Do not plot ROC curve when there are no actives or inactives.

See also: List of Changes in PyRx Version 0.5 and Earlier

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Last Updated on Thursday, 30 December 2010 13:41
e-LEA3D and ZODIAC PDF Print
Written by Sarkis Dallakian   

Thanks to Mark Fortner for sharing this article. It showed up today on my virtual screening feed from PubMed, but it's too good of an article to miss. Similar to AutoGrow, e-LEA3D is using fragments to built lead compounds. Building blocks are extracted from Comprehensive Medicinal Chemistry database by Symyx. It was interesting to find that besides DOCK Blaster there are also TarFisDock and SCFBIO servers that are using DOCK. Cloud Computing For Drug Discovery is an interesting subject and I knew that there are servers such as DockingServer, DrugFinder and GridSystems that are doing excellent job in this area. It's interesting also to mention that current version of e-LEA3D is using PLANTS for docking and Frog to generate 3D conformations. The most exciting part is that I rediscovered ZODIAC which is also a GUI for PLANTS. ZODIAC is very similar in spirit to PyRx in that it's an open source state-of-the-art tool for running molecular docking experiments. In summary, both e-LEA3D and ZODIAC are terrific tools for drug discovery.


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Last Updated on Thursday, 29 September 2011 09:30
ParaDockS PDF Print
Written by Sarkis Dallakian   

There is a new article in J. Chem. Inf. Model. that talks about ParaDockS. This is the only other docking program, besides AutoDock 4 and Vina, that is open source. Congradulations to ParaDockS team for making such a great product available! This means that PyRx can some day use ParaDockS and vise versa, so here I'll summirize main features of ParaDockS. First, it's using particle-swarm optimizer, similar to PSO@Autodock. Unlike, AutoDock 4, which uses force field-derived (AMBER) objective function, ParaDockS is using knowledge-based potentials. I look forward for the new develoments in this area.

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Last Updated on Thursday, 29 September 2011 09:30
List of Changes in PyRx Version 0.5 and Earlier PDF Print
Written by Sarkis Dallakian   

The following are list of changes in PyRx version 0.5 and earlier:

Version 0.5 - 25 March 2010

  • Added Save as Comma-Separated Values (CSV) tool for database tables.
  • Added plotting feature for database tables. This feature can be accessed through a toolbar button under Tables tab. By default, it opens up Table Plotting Dialog where a bar plot of Binding Energy versus Ligand (index) is shown. If you have PubChem BioAssay opened using open CVS button, this widget will also check to see if there is Outcome column in that table, and if so, it will color bars corresponding to "Active" compound red and bars corresponding to "Inactive" blue.
  • Changed default for maximum number of energy evaluations (generic algorithm parameter in AutoDock) from medium (ga_num_evals = 2500000) to short (ga_num_evals = 250000).
  • Added AutoDock PBS job submission progress dialog.
  • Fixed a bug that was causing problems when displaying molecular surfaces for docked conformations.
  • Added a dialog to select alternate conformation when making macromolecule file (pdbqt) for AutoDock.
  • Enabled Enthought's quality agent that can be used to get bug report and comments from a user.
  • Added Cancel option for AutoGrid Web Services.
  • Implemented flexible residues for AutoDock. This feature can be accesses by selecting residue(s) under Navigator -> Molecules and right-clicking on them. Select AutoDock -> Flexible Residues to create _flex folder under Navigator -> AutoDock -> Macromolecules with receptor pdbqt and flex.pdbqt. All docking to this receptor is then done with this flexible residue(s).
  • Updated Python to version 2.6 and ETS to 3.4.0.
  • The new installers delete previous installation folder, if any, before installing this new version.

Version 0.4 - 2 November 2009

  • Fixed TraitError: The 'cpu_num' (see Re: PyRx won't start).
  • Added AutoDockRemotePreferencesPage to allows users to change AutoDock and AutoDock service names. The defaults are set to Autodock_4.2.1 and Autodock_4.2.1.
  • Modified Remote Jobs Query in webSerives; it now updates the GUI after checking each job individually.
  • Made changes to AutoDockPage to make parsing and displaying docking results faster.
  • PyRx Table is populated when user clicks on that tab to speed up the startup time (see Re: How can I find the mistake).

Version 0.3 - 23 September 2009

  • When making AutoDock Ligands using Open Babel, it now logs problem causing cases.
  • Fixed Maximize action for Run AutoGrid page on AutoDock Wizard.
  • Local AutoDock executable paths can now have spaces in it.
  • Added splash screen.
  • Updated Enthought Tool Suite to version 3.3.0.

Version 0.2 - 20 June 2009

Version 0.1 - 23 April 2009

  • Fixed a couple of critical bugs including the one mentioned here.
  • Upgraded Enthought Tool Suite to version 3.0.2 and Open Babel to 2.2.1.
  • Added new AutoDock Execution Mode labeled Cluster (Portable Batch System) mode.


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Last Updated on Friday, 22 October 2010 13:26

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