Winner of new iPOD announced: A Winner has been selected from among Accelrys customers who responded to the customer support survey between the months of July 2008 and Dec 2008. The winner of the December 2008 drawing is Yi Li from Sanofi-Aventis. Congratulations Yi on your new iPOD!
Life Sciences Product training: Accelrys training offerings are available here.
Join us for the Accelrys User Group meeting February 18-20th! Full details are here.
Tips & Tricks
If you have created one or more DS subroutines (perl scripts) that you would like to be able to call from other DS scripts and you don't want to have to explicitly define them in each script you can add such subroutines to a .pm file and store that file in a specific location.
You would then add the following lines to each script you wish to call the subroutine in:
# add custom library:
use lib "c:/My Folder";
use myCommands;
Of course, myCommands.pm must be located in "c:/My Folder" and must be a valid Perl package.
You can refer to standard Perl documentation on how to create a Perl package, but here is a template (the "1;" at the bottom is important...): # Template package
package myCommands;
use Exporter;
our $VERSION = 2.1;
our @ISA = qw(Exporter);
our @EXPORT_OK = qw(test);
Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores
The authors used Discovery Studio and Catalyst tools for structure based design using pharmacophore screening. The authors write "The design of biologically active compounds from ligand-free protein structures using a structure-based approach is still a major challenge. In this paper, we present a fast knowledge-based approach (HS-Pharm) that allows the prioritization of cavity atoms that should be targeted for ligand binding, by training machine learning algorithms with atom-based fingerprints of known ligand-binding pockets. The knowledge of hot spots for ligand binding is here used for focusing structure-based pharmacophore models. Three targets of pharmacological interest (neuraminidase, 2 adrenergic receptor, and cyclooxygenase-2) were used to test the evaluated methodology, and the derived structure-based pharmacophores were used in retrospective virtual screening studies. The current study shows that structure-based pharmacophore screening is a powerful technique for the fast identification of potential hits in a chemical library, and that it is a valid alternative to virtual screening by molecular docking."
Pre-pend a new conformation to a trajectory for analysis. This Discovery Studio script lets you prepend a conformation, usually an initial conformation from a crystal structure to a trajectory for use in the Discovery Studio Analyze Trajectory tools. The script is present in the forums here.
Protocol of the Month
Auto Homology Modeling
This protocol does the following: Runs PSI-BLAST on a sequence then follows up with ALIGN123, Then Generates a Structure based on the sequence alignment. The Protocol can be downloaded here.
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