[ Linked Alignments and Structure ]

Objective

To make a protein model based on sequence homology.

Background

ICM has an excellent record in building accurate models by homology. The procedure will build the framework, shake up the side-chains and loops by global energy optimization. You can also color the model by local reliability to identify the potentially wrong parts of the model.

Instructions

1. Edit/Delete All . let us begin with a clear ICM session!
2. Homology/Load Example
3. Two sequences (ly6,CD59), one template structure (x) and an alignment (sx) should be loaded. Sequence CD59 is the sequence of the template structure called x.
4. Homology/Build Model and fill in the table using the drop down options. Warning minimize side-chains may take a few minutes.

Notes and things to try:

• The four built in loops are shown in red as default.
• Try displaying the model and the template in different colors or representations to observe any siginificant deviations between template and model.

Manual References (Web Links)

Homology Modeling

31.1.1 Linked Alignments and Structures

Objective

To select, display and label the conserved regions of the model.

Background

Within the ICM Alignment Editor there is a rich array of tools. Some of these tools allow selections between a linked alignment and a structure. The strength of consensus can be changed and selections can be made according to a variety of criteria. There will be an alignment symbol next to a structure in the ICM Workspace if the structure is aligned.

Instructions

Using the alignment from the previous lesson we will display and label the conserved residues between our model and the template in CPK format.

1. Change the strength of the alignment consensus to 50% in the ICM Alignment Editor.
2. Type in the consensus you wish to select. For example if you only want to select identical residues between the template and model type in X. Other symbols (such as #) from the alignment consensus line can be entered here if desired. You may wish to play with this and the alignment consensus value.
3. Click on the Select button and the residues selected will be highlighted with green crosses.
4. To label the residues select the display tab and select the label residue button.

Manual References (Web Links)

Alignment Editor