Secondary Structure – Coiled Coil

The Secondary Structure – Coiled Coil track predicts structures according to the formula of Lupas et al., 1991. You may use this track with the Transmembrane – Goldman-Engleman-Steitz track to predict transmembrane alpha helices.

To apply this track to the sequence:

In the Tracks panel, expand Secondary Structure and check the box next to Coiled Coil. The track will now be visible in the Analysis view

To edit track options:

Select the track in the Tracks panel. Open the Track Options section, which appears as follows:

• Threshold – threshold needed to determine a positive score in the region graph. 1.3 is the default value because it is the minimum score for a known coiled-coil. If you need less stringent coiled-coil predictions (e.g., for globular proteins), you may want to lower this to 1.1. If you want to predict very stringent coiled-coils, (e.g., for fibrous proteins), raise it to 1.5.

Click if you wish to return to the default value.