Protocol Custom protocol to model antibody loops for multiple proteins in Discovery Studio

JS 2021-11-12

PURPOSE: This is a modified version of the Model Antibody Loops protocol which comes standard in the Discovery Studio program. This version identifies and optimizes the CDR loop regions of multiple antibody structures. The user specifies a directory containing multiple model structures i.e. mol2 files. The protocol automatically searches recursively through all subdirectories of the directory specified. For example directory specified can be the Output directory of an Antibody Modeling Cascade job. The protocol will then perform the loop modeling for each input molecule. This protocol also allows the user to specify their own CDR loop definition.
Note, if the protocol is run from the Discovery Studio Client and the client is connected to a remote server, the Directory specified must be a path on the server, not the client. Under such circumstances it might be easier to run the protocol from the Pipeline Pilot Client and upload the files to a location on the server first.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install in Discovery Studio only, go to the Protocol Explorer, right-click over the folder you want to add the protocol to, choose Import, navigate to the location of the Batch Model Antibody Loops.ppxml file and enter it as the File Name.

DISCLAIMER: This custom script is compatible with Discovery Studio 2021. The code or software provided by Dassault Systemes Biovia Corp. ("BIOVIA") in conjunction with this request is provided under the same license terms and restrictions as the underlying BIOVIA software it is intended to be used with, including license duration and location based restrictions, with the following exceptions. This software is provided on an AS-IS and AS-AVAILABLE basis with no guarantee or warranty, and is not subject to maintenance, updates, or support. When your license to use the underlying BIOVIA software terminates, your license to use this software will also terminate. BIOVIA makes no warranty that this software will be usable for any purpose.