PURPOSE: Uses the MODELER program. This protocol is a variation on the Build Homology Models protocol.

This version takes a Sequence Alignment and single Template Structure as input. The Sequence Alignment must contain the Template sequence. All additional sequences in the alignment will be modeled against the input Template. The protocol can use the existing alignment to build the models or perform pairwise alignment using Align123 on each model sequence and the template sequence to generate a new sequence alignment prior to building the models.

Set Copy Ligands to copy the ligands of the templates to the models as rigid body. If some sequence segments of the model sequence are not aligned with the templates, Refine Loops can be used to build additional refinement models for these segments.

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 Build Homology Models for Multiple Sequences.xml file and enter it as the File Name.

REQUIREMENTS: Discovery Studio Component Collection.

KEYWORDS: homology modeling, sequence, alignment

DISCLAIMER: This custom protocol is compatible with Discovery Studio 2.5 and Pipeline Pilot server version 7.5.2 (SES). 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.