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Surface Analysis of a Protein Using CASTp
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 Procedure

 

A graphic user interface allows users to request a CASTp calculation. The user can provide the input in either of the two ways. One can either upload the structure of the protein or can type the four letter PDB code of a protein structure if it is available from the Protein Data Bank. In this case the CAST server will fetch that structure. The structure of the molecule to be uploaded must be in PDB format.

 

For details regarding the retrieval of input check the simulator tab

 

Analysis of the protein using CASTp

 

Home page of CASTP is shown in Figure 1.Give the protein ID (PDB ID) in the box provided and clicks on the ‘search’ button (figure 1).

 

 

 Figure 1

 

Click on the search option to get the result

 

Results will be appearing on the new page. A table of all the annotated sites is displayed on the right hand side of the result page. This table reports the following information: the database from which the annotation was derived from, the annotation keyword from the database, the position of the annotation on the sequence of the PDB structure, the three letter amino acid code of the annotated residue, the identifications of the annotated residues in the pocket is located and a brief description of the annotation. User can also get result through the email in a text file with all the information. The protein structure can be viewed as wireframes, strands, cartoons or ribbons. The result page is shown in Figure 2.
 

 

Figure 2

 

Pocket information:

 

By clicking each pocket from the pocket information (which is shown in left of the window), the pocket residues would be represent in different colors based on their ids. It will shows the pocket information like area, volume, and the aminoacid sequence which is highlighted by the color regarding to the pocket color.

 

Figure 3

 

The result page gives different optionsto interactively visualize the surface pocket. This is a very good method to explore the surface features of a protein. For example, each time you can check and see if a specific residue is in a pocket and what that pocket looks like.

 

 

 This experiment uses the CASTp online resource, available through http://cast.engr.uic.edu

 Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz, and Jie Liang. 2006. CASTp: computed atas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl. Acids Res., 34:W116-W118.

 

 

 

 

 

 

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