PURPOSE: This is a batch version of the 'Model Antibody Loops' protocol available with the DS release. This version accepts multiple Input Protein Molecules. As with the released version it uses BLAST to perform a similarity search against pre-compiled antibody domain and CDR loop databases to identify Complementarity Determining Regions (CDR) in the Input Protein Molecules. An alignment is created for each CDR loop against its best hits from the BLAST searches. Set Build Models to "True" to use MODELER to generate homology models of the structure based on the hits.
The following steps are performed:
- Identifies antibody loops
- Builds models
Steps in italics may be skipped depending on settings.
Note:
- CDR loops will be stored as residue groups in the output DSV file.
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 Model Antibody Loops Batch.xml file and enter it as the File Name.
REQUIREMENTS: Discovery Studio Embedded Collection. DS Protein Modeling
DISCLAIMER: This custom protocol is compatible with Discovery Studio 3.1 and Pipeline Pilot server version 8.5. It is provided "as is" and is NOT supported by Accelrys nor is it warranted for any purpose whatsoever. The user assumes responsibility for any malfunctions or bugs.
