PURPOSE: This protocol takes a set of pdb files and a reference protein as input. Each  pdb file is structurally aligned to the reference using 3DMA and an alignment  file is produced. Each structure is superimposed on the reference according to  the generated alignment using either Main-chain atoms or C-alpha atoms. The aligned structures are output as individual pdb  files and as a single dsv file. The output also contains the pairwise sequence alignment (bsml) files generated for each input pdb file with the reference.

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 Align Proteins to Reference.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.