Prime User Manual - ISP

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Chapter 5: Comparative Modeling: Build Structure
5.4 Saving and Exporting Built Structures
When building is complete, the built structures can be added to the Maestro project by clicking
Add to Project Table. Once you have added the structure to the Project Table, you can refine the
structure by choosing Applications > Prime > Refinement in the main window. You can also
export any Project Table entry, such as a built structure, to a file of another format. For information
on exporting structures, see Section 3.2 of the Maestro User Manual.
5.5 Technical Notes for the Build Structure Step
The Build Structure step uses the following resources and methods:
• The OPLS_2005 all-atom force field for energy scoring of proteins as well as for ligands
and other non-amino-acid residues.
• A Surface Generalized Born (SGB) continuum solvation model for treating solvation
energies and effects.
• Residue-specific side-chain rotamer and backbone dihedral libraries, derived from the
non-redundant data sets extracted from the PDB, and representing values most commonly
observed in protein crystal structures. The libraries allow for both the evaluation of existing
rotamer/dihedral values and the systematic prediction of new ones.
Both Build Structure and the step that follows, Refine Structure, can treat the 20 standard
amino acids as well as modified residues and ligands.
Model building uses the following procedure:
1. Non-conserved residues are mutated to the desired identity. Side chains are added by
finding the first rotamer in the library that does not produce a clash.
2. Insertions, deletions, and template transitions are built. These are cases in which the
backbone itself needs to be reconstructed, either due to gaps in the alignment or template
transitions that produce gaps in the 3D structure. These gaps are closed by reconstruction
of the affected region ab initio, using a backbone dihedral library. If no reasonable conformation
can be generated that closes the loop structure, the region being reconstructed
will be expanded until closure is possible.
3. Gap reconstruction is done by finding any single loop conformation that closes the structure
and is physically reasonable. If multiple conformations are found, the one that deviates
from the template structure as little as possible is chosen. No attempt is made to
perform an exhaustive optimization of the region.
Prime 2.1 User Manual