PURPOSE: This protocol is a combination of several standard DS protocols. Given an input sequence, the first step in this protocol is to run the Identify Framework Templates. The hits which are returned as the best "Overall Templates" (covering the heavy and light regions) are read in as pdb files and are cleaned up so that only one heavy and light chain complex are retained for each hit. These are then run through the Analyze Protein Interface protocol to identify the residues at the interface of Light and Heavy chain domains. The sequences of the best overall hits are also run through the Annotate Antibody Sequences and the sequences are aligned to the target sequence.

Finally, by knowing the alignment of each template to the target sequence and the interfacing residues in the template structures, it makes it possible to calculate the percent identity and similarity for just those interfacing residues in the template and those they are aligned to in the target. And instead of considering all the interfacing residues, it only considers those in the variable regions of the chains. The percent identity and similarity are reported in a table in the Report.htm for each template.

The output includes the aligned sequences and the aligned structures (in which there is a new group called Interfacing Residues in Variable Region). Note, the structures are aligned using the full length sequence alignment. Many of the output files generated for the individual steps are moved to the Intermediate folder.

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

Interface of overall Antibody Framework hits.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Embedded Collection.

DISCLAIMER: This custom protocol is compatible with Discovery Studio 3.5 and Pipeline Pilot server version 8.5 CU3. 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.