RasCtrl

RasCtrl Sample: MotMan

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MotMan is a C# application using RasCtrl components to visualize and manipulate motifs. It demonstrates how to overlap same-structural motifs in different proteins in a single RasCtrl and how to synchronize rotations of motifs among several RasCtrls. These functions help users to understand the spatial arrangements of motifs and compare the structure of motifs in different proteins. 

Spatial motifs are local substructures within a protein. These substructures, composed of a small number of amino acid residues, often have conserved spatial arrangements across a group of proteins of the same function. A central tenet of modern biology is that a protein's function is determined by its structure. The Motif Space project developed automated techniques to identify spatial motifs in proteins.

This application visualizes motifs with same structure in four proteins, which are identified by the proposed frequent subgraph mining methods. A motif is represented by the protein name, the chain ID, and a list of amino acid residue numbers. The four motifs visualized in the application are listed as following.

Press the Load button to load the four proteins. The default folder containing the PDB files are in the folder C:\RasCtrl\data. If the PDB files are in different folder, please modify the loading part of the source code. Two proteins are loaded to the left RasCtrl and two to the right. The screenshot after loading is shown as following.

Press the Show Moitf button to highlight the motifs. A motif is visualized as several balls, which represent the alpha carbons of the amino acids that constitute the motif. The screenshot with the highlighted motifs is shown as following.

Press the Align Motif button to align the motifs to same position and orientation. The alignment is performed based on the positions of alpha carbons in the amino acids that constitute the motif. The position alignment is achieved by using RasMol commands. The orientation alignment is achieved by using the GetMotifCaPos and AlignMotif methods. Please refer to the sample code for more details.

In the orientation alignment, a motif is chosen as a reference. The positions of the alpha carbons in the reference motif are obtained by calling the method GetMotifCaPos. The orientations of the remaining motifs are aligned to the reference motif by calling the method AlignMotif, which takes the alpha carbon positions of the reference as the input. 

After alignment, the motifs in a window are overlapped. The motifs in different windows have same orientation. The rotations of motifs can be synchronized by checking the Synchronize Rotation option. The screenshot after alignment is shown as following.