Refining Protein Structures

The Refinement module in Prime is used to refine protein structures. It can be used for loop refinement, side-chain prediction, minimization, rigid-body minimization, hybrid Monte Carlo conformational searching, binding site refinement, and energy analysis at the current geometry of the protein structure. The refinement can be performed in implicit solvent, an implicit membrane, or both.

Each task from this module is presented in Maestro as a separate panel, which you can open in the Task tool by choosing Protein Preparation and Refinement → task.

Model structures built in the Build Homology Model Panel usually require further refinement. If there are insertions or deletions in the alignment between query and template, it is recommended that you perform a loop refinement, since insertions and deletions are most frequently found in loop regions. As another example, if you have added a water molecule to the binding site of the protein, you can run a refinement on the composite entry.

Maestro provides several tools to analyze protein structures, which can give information on the parts of the structure that may need refinement. See Protein Tools for more information on these tools.

For information on running the Prime refinement tasks from Maestro, see the help topics, which are listed below.

• Refine Loops Panel
• Predict Side Chains Panel
• Prime — Minimize Panel
• Minimize as Rigid Body Panel
• Hybrid Monte Carlo Panel
• Refine Protein-Ligand Complex Panel
• Calculate Energy Panel

You can also run refinements from the command line, with the prime command. See prime—Build and Refine Protein Structures for details of the command syntax.