Discovery Studio contains a protocol which annotates antibody sequences. This protocol is useful to annotate an antibody structure. It also performs analysis on the H and L chain interface and reports the angle between the VH and VL residues.

PURPOSE: Extracts the sequence from the Input Antibody Protein and runs the Annotation Antibody component. Then determines the interfacing residues for each chain based on the change in the solvent accessible surface area when the chain is in complex and out of complex (taking into consideration the Percent Contact Area Threshold). The interfacing residues and annotations are all represented as groups in the output dsv file (under Antibody Groups). Note, the protocol only runs on one input molecule at a time.

In addition, this protocol calculates the angle between the VL and VH chains as both the angle between the best-fit vectors of each chain and best-fit planes of each chain. This step is performed using the R package and therefore, R must be installed on the DS server.

USAGE: This protocol can be launched from both the Discovery Studio and Pipeline Pilot clients. To install use the Pipeline Pilot Client, go to the User Explorer Window right-click and choose Import, navigate to the location of the Annotate Antibody Structure and VH VL angle.ppxml file and enter it as the File Name. The protocol will then be available from the DS Client under the User folder.

REQUIREMENTS: Discovery Studio Collection. Installation and configuration of the R Software package from https://www.r-project.org/ . To configure R, from the PP Admin Portal set the Global Property R_exe to the location of R.exe .

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2025 and Pipeline Pilot server version 2025. 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.

An example of the output dsv file produced by this protocol. Notice the groups 'ChainH_Interface_Residues' and 'ChainL_Interface_Residues', the green and orange lines which represent the best-fit lines passing through the VL and VH residues. and the angle values reported in the Data Table.