Blog Archives

Cell-Dock: High performance protein-protein docking

8/10/2012

New protein-protein docking sofware released in the journal Bioinformatics. Excerpt from the abstract:

"Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200x, while achieving results of similar qualityAvailability and implementation: The source code is released under GNU General Public License version 2 and can be downloaded from http://mmb.pcb.ub.es/~cpons/Cell-Dock"

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On the quality of X-ray structures used in drug design

8/2/2012

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A great blog post by Ash Jogalekar on his "Curious Wavefunction" website highlights the importance of the quality of published crystal structures and that caution should be taken when using them in drug design projects.

"These structures can hide flaws that don't become apparent until they are actually revealed through analysis. Worse still, there may be flaws that never become apparent because nobody takes the trouble to look at the original data."

All lab members should read the paper "Essential considerations for using protein–ligand structures in drug discovery" by Openeye.

Metrics that should be used apart from the resolution of the structure include:

Completeness of data (if you have a structure that is only 80% complete you should start worrying)
A difference between R-free and the R-factor of more than 0.45 for a structure with resolution 3.5 A or more, is alarming.
Visualization of the actual electron density, especially for ligand atoms (in some cases there were crystal structures reporting ligands that did not show any electron density!)

For more info read: http://wavefunction.fieldofscience.com/2012/08/protein-ligand-crystal-structures.html

Zoe

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Webinar: Accessing ChEMBL Web Services via Workflow Tools

8/1/2012

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One of our previous speakers, Dr. George Papadatos, is hosting a webinar on accessing ChEMBL REST web services via KNIME and Pipeline Pilot at 3.30 pm BST on Wednesday, 8th August 2012.

Please email George in advance in order to register for this webinar.

Zoe

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How to set up an email subscription form onto any website with an RSS feed

8/1/2012

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Do you want to set up an e-mail subscription where readers will be automatically notified by e-mail when you update your blog or any other site you maintain?

First you need to find out the RSS feed of your website (most websites have that feature).
Then, the best option is the FeedBurner email subscriber widget available at http://feedburner.google.com.

You'll need to create an account or sign in using your Google account and provide Feedburner with the RSS feed address for your blog. You can then click on the Publicize tab at the top of the page and select E-mail subscriptions on the left. Copy the code Feedburner provides and paste it into your website as HTML code.

Taken from https://getsatisfaction.com/weebly/topics/setting_up_a_weebly_blog_for_email_updates

Zoe

5 Comments

Cell-Dock: High performance protein-protein docking

On the quality of X-ray structures used in drug design

Webinar: Accessing ChEMBL Web Services via Workflow Tools

How to set up an email subscription form onto any website with an RSS feed

Alexis, Michalis, Danai, Panos, Sotiris, Nastazia, Vassilis, Zoe

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