We are pleased to announce the release of PyRx 0.9.1. This is a minor bugfix release. PyRx 0.9 users, please use PyRx > Help > Check for Updates…  menu to update. The following is a new feature and a bug fix implemented for 0.9.1 release: [r151] Added stereo rendering option to 3D scene. Click on…

We are pleased to announce the release of PyRx 0.9. The following are new features and bug fixes implemented for 0.9 release: [105] Vina Wizard is now using the number of CPUs (–cpu option). Please use Edit > Preferences and enter Available CPUs to specify this number. By default, PyRx sets it to the number…

I wrote this small script that can be used to rotate molecules in PyRx. You can try it by downloading rotate.py and then use File → Run Python Script menu from PyRx to run it. To stop this rotation, click on Python Shell tab under Controls panel, type stop() and hit Enter. The following is…

This post explains how to install NVIDIA proprietary drivers on CentOS 6. By default, CentOS 6 comes with nouveau drivers, which for 3D (OpenGL) rendering, is order of magnitude slower that NVIDIA’s proprietary drivers.  For instance, I had glxgear running at round 400 frames per second (FPS) before installing NVIDIA proprietary drivers and at around…

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…

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…

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…

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…

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…