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Dec 10 2020

T97-2020: Notification regarding RCSB Structure Search protocol in BIOVIA Discovery Studio

BIOVIA Discovery Studio

Program

BIOVIA Discovery Studio 2018, 2019 and 2020

Operating System

All operating systems supported for BIOVIA Discovery Studio

Background

The RCSB PDB legacy APIs will be discontinued on the 9th of December 2020. Therefore, running the RCSB Structure Search protocol available in Discovery Studio 2018, 2019 and 2020 may result in ‘No hits found’ or an error.

Solution

A new modified version of the RCSB Structure Search protocol which uses the new RCSB JSON APIs can be found <here>.

The same or equivalent searches are supported, wherever possible. The Motif search now allows searching using Prosite-type motifs or regular expressions, and can be applied to protein, DNA or RNA sequences. However, sequence similarity searches and the HasLigand filter are no longer supported.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in the Discovery Studio server

  1. Go to the Protocols Explorer, right-click over the folder you want to add the protocol to and choose Import…(it is recommended to install in your User folder)
  2. In the panel that appears navigate to the location of the downloaded RCSB Structure Search (JSON).ppxml file and enter it as the File Name. You may be required to right-click over the folder and choose Refresh to see the new protocol.
  3. Once the protocol has been added on the server you may use it by double clicking on the protocol name and running it from the Parameter Explorer.

NOTE: This updated protocol may be used in Discovery Studio versions 2018, 2019 and 2020.

How to contact BIOVIA Support

If you have any questions, please contact BIOVIA Support.