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DISCOVERY STUDIO

Optimize your drug discovery process with a flexible application that delivers  predictive science to its required depth.

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July-August 2008

Accelrys Discovery Studio Newsletter

News and Information
DS Tips and Tricks
DS Community Forum Highlight
Script or Protocol of the Month

News and Information

  • Discovery Studio 2.1: New Science and Customized Workflows for Drug Discovery Research Webinar series
  • Webinars for the life sciences:
    Web seminars are announced on our web pages periodically. These seminars are offered on a wide variety of topics and are usually recorded. The recorded webinars for life sciences can be found here
  • Product Training :
    Web based and on-site trainning is available for most Accelrys Products. Details for product training options are described here

Tips & Tricks

Discovery Studio scripts have a built in syntax checking option. Syntax checking can be initiated by clicking on the "check" icon next to the blue arrow button that runs a script..

Running scripts can be stopped by pressing the red X button next to the green "go" button . .However, this button will be grayed-out when the script windows is active (selected). Simply click on the 3D (or Sequence) window to change the active window.

The effect of running a script can be undone by selecting Edit/Undo.

Community Forum Highlight

Pipeline pilot versions 6.1.6 and later contain a very modular method of extending a protocol so that it can operate using coarse-grained parallelization. A recent posting to the forums page demonstrates a modification of the standard Prepare Ligand script by transforming it into a script in which multiple processors can be used. Follow this link to the posting in the Accelrys Forums for Prepare Ligand

 

Script of the Month

This script mimics an old Insight II feature but does more. The group_secStr.pl script creates groups for each of the helical, sheet and other secondary structure segments found in a protein. This can be very useful for locating specific secondary structure domains then performing operations on them, for example adding constraints. It is a nice script to demonstrate the use of the ability to define "groups" using a Discovery Script. The script returns one group definition for each secondary structural element that meets the cutoff criteria. This script will also print the residue range of each secondary structure element that is found. The full script can be downloaded from the forums here. The image below is the result when the first two groups are shown using the "tube" display. The second group (helix_2) is shown still selected (yellow).

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