October 2009

Accelrys Discovery Studio Newsletter

News and Information

• An update for Discovery Studio 2.5 Client is now available!

  The Discovery Studio 2.5.1 update contains several client side enhancements. A complete list of enhancements and corrections is available.
  Choose one of the following two options to obtain the update:
  1) Download the update from the Discovery Studio 2.5 update download page:
  http://accelrys.com/downloads/updates/discovery-studio/dstudio25/dstudio251.html
  2) From within the Discovery Studio Client 2.5, access the Help menu and select “Check for Updates”.
  

• We are pleased to announce the latest release of the FREE DSVisualizer 2.5 for Windows and Linux workstations. Discovery Studio Client is built upon the free DSVisualizer which offers extra functionality, for a complete list of features available in the free DSVisualizer 2.5, please refer to the product datasheet. This free application is a great way to collaborate and share modeling data with project team members!

• With the free DS Visualizer download, you additionally receive the FREE DS ActiveX control - an application that allows you to easily embed live 3D structures in Microsoft® PowerPoint, Word, and html documents, enabling you to create and present powerful presentations and animations! To download your copy of the DSVisualizer and the ActiveX control, please visit the DS product page.

• Already using the free DSVisualizer? We would love to hear your feedback and comments on the product. Please visit our newly launched Accelrys Blog and share your thoughts on the freeware! While you are there, cast your vote on your favorite free 3D visualizer and see the results.

• We are pleased to offer a series of scientific webinars covering the new functionality in Discovery Studio 2.5. Run by the Accelrys European scientists, this webinar series offers the convenience of a preferred time zone for our European customers! Please register to join these live sessions and participate in interactive demonstrations and Q/A sessions. To register and sign up for the events, please visit: http://accelrys.com/events/webinars/european-webinar-series/

• With the growing number of publications citing Accelrys modeling and simulations tools, we have recently updated our website with select references included under several categories.

Tips & Tricks

Customize default parameters for any protocol from Discovery Studio

Often there are some parameters in frequently use protocols that you find you change every time you run the protocol. You can easily save this value as the new default. For example, open the Dynamics (Production) protocol. Change the Production/Steps parameter to 10000, and the Save Results Frequency parameter to 500. Finally, right-click and select "Save Protocol Settings". The parameters you have set will now be defaults when the protocol is next opened. You can restore the original defaults by right-clicking and selecting "Restore Original Settings".

Featured Journal Article

A. M. Abu Hammad, M. O. Taha., ,J. Chem. Inf. Model. 2009, 49, 978–996, "Pharmacophore Modeling, Quantitative Structure-Activity Relationship Analysis, and Shape-Complemented in Silico Screening Allow Access to Novel Influenza Neuraminidase Inhibitors"

The fight against various forms of the flu have been in the news a lot recently. In this month’s featured journal article researchers are using Accelrys products to find new classes of inhibitors enzyme neuraminidase which is responsible for viral release from infected cells.

From J. Chem. Inf. Model. 2009, 49, pg 985 Figure 5. (A) The pharmacophoric features of B-2-6. Light blue spheres represent hydrophobic features, red spheres represent positive ionizables features, while green-vectored spheres encode for hydrogen-bond acceptor. (B) Inhibitor 136 (structure C, IC50) 0.3 nM) fitted against B-2-6 and combined with the corresponding molecular shape.

In their approach, the authors confront directly the difficulties of finding inhibitors based on transition state analogues. They succeed in finding novel Influenza neuraminidase inhibitors through the use of multiple techniques including Discovery Studio pharmacophore (Catalyst) tools, such as, 3D QSAR HypoGen, Shape features, , and QSAR tools (Cerius2).
On-line access to this article is available here.

Community Forum Highlight

Find residues with non-integer charge and find charge sum of the selected atoms

When a structure contains non-standard residues it is possible that customization of partial charges will be necessary before running molecular dynamics. Having a zero net charge for a system is particularly important when running molecular dynamics calculations using the Ewald Electrostatics option. A script has been written that compares the formal and partial charges for each residue and identifies residues for which these do not match. Once a problem residue has been found you can also select fragments of this residue and rerun the script to get the sum of the selected charges.

The check_chargesv2r1 script can be downloaded here.

Protocol of the Month

Dynamics (Production Loop) generates multiple production trajectories. It is useful for long simulations where a single trajectory would be unwieldy in Discovery Studio.

This protocol allows you to run multiple production simulations from a single protocol. Only the final stage's trajectory is returned in the dsv file, but CHARMm format dcd files are saved for all stages, and thus can be viewed or analyzed. The protocol itself is implemented using a Pipeline Pilot loop. Loops are a good solution for a protocol that requires a large number of passes through the pipe for each input structure. The protocol can be downloaded here.