Dockground

Rotamers and Rotamer Transition Probabilities in Protein Binding

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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.

JSmol Instructions

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.

References

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.

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