How to Use This Application
- Select an amino acid using the dropdown menus on the navigation bar on the top of this page.
- Visualize a specific unbound rotamer by clicking one of the buttons in the 'Select' column.
- Click on the checkboxes in the "Show" column(s) to display and hide rotamers.
- Adjust the transparency of rotamers using the slide bars in the "Transparency" column as needed.
- Click on the checkboxes in the "Χ" columns to draw arrows around the corresponding dihedral angle.
- To change the coloring scheme of the visualizer, click on "Colors" in the navigation bar.
- Mouse and Keyboard
- Left-Click + Drag: Rotate the Model
- Scroll: Zoom-In and Zoom-Out
- Shift + Single Left-Click: Zoom-In and Zoom-Out
- Shift + Double Left-Click: Translate Model
- Touch Screen
- Drag One Finger: Rotate the Model
- Pinch-In or Pinch-Out: Zoom-In and Zoom-Out
- Drag Two Fingers in the Same Direction: Translate Model
Conformational changes in the side chains are essential for protein-protein binding. Rotameric states and unbound-to-bound conformational changes in the surface residues were systematically studied on a representative set of protein complexes. The side-chain conformations were mapped onto dihedral angles space. Rotamers were defined as the most probable conformation in a cluster. Probabilities of the rotamer transitions upon binding were calculated.
Tatsiana Kirys, Anatoly M. Ruvinsky, Alexander V. Tuzikov and Ilya A. Vakser
Rotamer libraries and probabilities of transition between rotamers for the side chains in protein–protein binding. Proteins 2012; 80:2089–2098.