Motion Library

The Motion Library consists of over 500 animated and annotated macromolecular motions illustrating structural conformational changes. The intermediate structures in the animation are an interpolation between two experimentally-determined protein conformations calculated by the Morph Server.

The structures that define each Motion Library motion are chemically plausible, meaning that bond lengths, bond angles, and steric interactions within the structures are confined insofar as possible to reasonable geometries. The models do not include kinetic or other dynamic considerations. Nevertheless, the interpolated intermediates are likely similar to a subpopulation of the biologically-relevant conformational change intermediates (Krebs and Gerstein, 2000).

Annotations in the Motion Library are derived from the Protein Data Bank (PDB), the CATH protein structure classification database, and the Gene Ontology (GO) database. Annotations are based on the accurate assignment of PDB identifiers for the first and last conformations in the motion.

The following video is a brief introduction to the Motion Library:

To open the Motion Library:

Do either of the following:

• Use View > Motion Library
• Press Ctrl+Alt+L (Windows) or Option+Cmd+L (Macintosh).

To use the Motion Library:

In the Motion Library Window, motion previews appear as image thumbnails. These represent all of the protein motions in the Library as animated previews grouped by CATH Architecture (i.e. the “A” term of the CATH hierarchy: “Alpha-Beta Complex,” “Propeller,” etc.). Motions without a CATH ID are grouped into an “Uncategorized” section at the bottom.

Underneath each preview are partial PDB IDs of the first and last structure sequences in the animation. Each preview group is part of an expand bar that can be collapsed or expanded as desired.

Task	How To
To open a motion in the main viewer	Double-click on its preview.
To expand or collapse all categories (expand bars) simultaneously	Click the Expand/Collapse All Categories tools () under the Search button.
To view the names and PDB IDs of the first/last structures	Hover over the preview.
To view the full PDB IDs of the first/last structure	Hover over the partial ID listed below the preview.
To search for a particular motion	Use the Find field and associated Search button. These let you perform a simple (non-Boolean) “exact term” search of the Motion Library. After executing a search, only the motions that match the search term will remain visible in the preview area. If your search term contains a misspelling, you will be redirected to a help dialog. After performing a search, clicking the “x” icon () to the left of the Search button clears the results and makes all motions visible again in the preview area.
To view detailed information about a motion	Click once on the motion’s preview to display its information in the Information Panel.The information appears in three expand bars: First Model, Last Model, and Source. Some information is available for all motions in the Motion Library. CATH and GO information is shown if available, and links to the corresponding web pages. The PDB ID links to the entry in the RSCB Protein Data Bank.