Theory

The protein health option calculates the energy strain of a structure in ICM. It is generally a good idea to investigate the energy strain of any protein structure before undertaking such processes as docking. It is also essential to use this tool after making a model (see Molecular Modeling) to identify strained regions within your model and then some optimization procedure can be undertaken to rectify the problems.

The protein health option calculates the relative energy of each residue for a selection and colors the selected residues by strain.

This macro uses statistics obtained in the following paper Maiorov, V.N. and Abagyan, R.A. (1998) Energy strain in three-dimensional protein structures Folding and Design, 3 , 259-269.

To use the Protein Health option your structure must be converted into an ICM object (see Converting to ICM Object)

Next, make a selection of which residues you wish to analyze (see Making Selections).

• Tools/3D Predict/Protein Health and a window as shown below will be displayed.

• The scale of the coloring can be changed by altering the value within the trimEnergy data entry box.
• Click OK and the structure will be colored according to energy strain (red - high) and a table of residue energy will be displayed in a table.
• To reactivate the screen click the Go button in the bottom left hand corner of the GUI display.

The Protein Health option returns a table of energies for each amino acid in the selection:

The Protein Health option returns a plot of energies for each amino acid in the selection: