Home Blog
ConnectomeViewer and Spatio-Temporal Simulation Environment (STSE) PDF Print
Written by Sarkis Dallakian   

I was looking for a sample code and found Nullege search engine for Python source code to be very useful. There are other search engines that do similar work, such as Google Code Search and Koders.com, however, Nullege seems to be the best one for Python. I have found the following excellent projects that I would like to share. The first one is called ConnectomeViewer and it's an amazing tool for brain research. The second one is called STSE and it provides spatio-temporal simulation environment for biological systems. It's nice to see that they are both using Mayavi for 3D Visualization. Since PyRx is using Mayavi too, this means that our users will be able to transfer their skills seamlessly between these tools. I'm looking forward to seeing other uses of Mayavi and 3D Visualization in life sciences.

Add a comment
Last Updated on Monday, 14 February 2011 13:43
PyRx 0.8 Release Announcement PDF Print
Written by Sarkis Dallakian   

I'm pleased to announce the release of PyRx 0.8. Here is what's new in this new release:

Version 0.8 - 30 December 2010

[84] Implemented Vina Web Services client and added remote executaition mode for Vina wizard.


[83] Changed web service URI from http://ws.nbcr.net to http://kryptonite.nbcr.net. Opal client distributed with PyRx is compatible with Opal2 services running on this new server.

[80] We now show ScrolledMessageDialog with TraceBack when PyRx fails to start.

[76] Exporting SDF in Analyze Results allows to specify the Number of Poses to Retain. This option is available through Edit -> Preferences. In the case of Vina results, we sort the result using Vina Binding Affinity before saving the result. For AutoDock 4, sorting is done using Binding Energy.


[75] Implemented update feature available through Help -> Check for Updates menu. This enables users to get the latest features and bug fixes more easily. http://pyrx.scripps.edu/images/75_update.png

[74] Made a number of important changes and bug fixes related to flexible residue generation and docking. In particular the names of flexible and rigid parts of a macromolecule now ends with '_flex.pdbqt' and '_rigid.pdbqt', respectively. http://pyrx.scripps.edu/images/flex_rigid_74.png

[71] Users can now save docked structures and binding energies as SDF (Structure Data Format). Thanks to Martin Indarte post in the forum: SDF with binding energies/scores


[69] Switched back to using wx.TextCtrl in Text editors. This widget can now handle large files (> 5MB - tested with wxPython-2.8.11).

[66] Included an option for exhaustiveness in the Vina Wizard thanks to Martin Indarte post in the forum: Can I change the exhaustiveness in VINA wizard?

See also: List of Changes in PyRx Version 0.7

Add a comment
Last Updated on Monday, 10 January 2011 16:06
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.

Add a comment
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

Add a comment
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.


Add a comment
Last Updated on Thursday, 29 September 2011 09:30

Page 5 of 8
Get PyRx