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…

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…

Here are the results of a new PubChem BioAssay AID: 2427 with 42 compounds (22 active, 2 inactive and 18 inconclusive). AutoDock did a perfect job here giving favourable binding energy for active compounds compared to inactives. As a result, we have a prefect ROC curve here. I made the makers bigger so you can see…

I’ve got another email from My NCBI (Subject: What’s new for ‘BioAssay – Limits: Protein 3D Structure). It was about AID: 2353 – qHTS Assay for Inhibitors of RecQ-Like Dna Helicase 1 with 23 active and 1272 tested compounds. There are 2 Links for Protein Structure corresponding to open and closed conformations. I run virtual…

When preparing ligands for docking PyRx users can select between PyBabel (MGLTools) and Open Bable partial charges using Edit -> Preferences menu. See PyRx Screencast – Open Bable for details. PyRx is using PyBabel charges, by default. I run the dataset from my previous blog post, using Open Bable, to see if I can get…