Article ID: 272 - Last Modified: May 1, 2012
A homology model built on a DNA-containing template has all the DNA bases disconnected. How can the model be built with connected DNA strands?
From Suite 2011 on, this should no longer be an issue.
In earlier releases, Prime treats the bases as heteroatoms, and thus sees each base as an individual 'ligand'. In order to have them all connected you will have to change the template structure to have DNA strands as single residues. Use the Residue Properties panel to give each DNA strand a single residue name and number, then use the Atom Properties panel to set unique PDB atom names for the atoms in the strand. After making these changes for all DNA strands, export the structure as a PDB file and use this modified PDB file as the template for model building.
Keywords: Prime, structure prediction, DNA, homology model, Maestro
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