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DISCOVERY STUDIO

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September 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

  • Life Sciences Product training Accelrys training offerings are available here.
  • Conferences: Accelrys will be present at the "Latest Advances in Drug Discovery Informatics " conference being held at Bryn Mawr College, Philadelphia October 13 through 17th. Please visit us at our booth where we will be demonstrating Pipeline Pilot and new algorithms/science in Discovery Studio2.1, including fragment-based design, antibody modeling, protein pK prediction, virtual screening, compound profiling, and medicinal chemistry workbench. Workflow customization will be highlighted with the DS Developer Client. More information can be found here.

Tips & Tricks

Discovery Studio has many methods to modify atoms or build complete small molecules. One of the easiest ways is to use the Sketching Toolbar. This toolbar is not enabled by default so this feature is often overlooked. The toolbar is enabled from the DS View pulldown (View > Toolbars > Sketching). The tools are fairly intuitive, but the details are described in the DS Help (Help/Help topics). From the Search tab or the Index tab locate and view the "Sketching Toolbar" documentation. Also remember, atoms can be mutated to any of the commonly used elements by selecting the atom then typing the element letter using your keyboard. Similarlly, bonds can be changed by selecting a bond and typing a number (4=partialdouble/aromatic). Other methods are described in the "How to work with small molecules" document.

Community Forum Highlight

A DS script that reads in distance and dihedral constraints from a file then color-codes the constraint monitors based on how the constraints agree with the current conformation has recently been added to the forums. Several input formats are supported. You can learn more about this script here.

Protocol of the Month

This month we feature a DS SCRIPT that has been converted to a protocol (Mutate Amino Acids) to allow the key parameters to be set interactively. It is a good example to highlight the protocol components that are needed to interact with the DS scripting language. In this example the task is to mutate selected residues of a protein. The key input parameters required are the aminoacids to be mutated and the replacement aminoacid residue type. In the protocol, the selected residue input(s) are recognized from the selections or chosen from a table of all amino acids. The available replacement residue types are also selected from a list of all valid aminoacid types from a GUI. The protocol can be downloaded here.

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