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tutorials:mali_tutorial [2015/09/16 15:57]
hafsa 		tutorials:mali_tutorial [2015/09/22 14:07] (current)
hafsa [A Short Introduction to CATH and Gene3D]
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 Each level has a **CATH code** associated with it. Have a look at the following: Each level has a **CATH code** associated with it. Have a look at the following:
  
-{{:tutorials:cath_code.png|}}+{{:tutorials:class_3_screenshot.png|}}
  
 In this example, the CATH code for the domain 1tsrB00 is 2.60.40.720. The **2** refers to the class to which the domain belongs (mainly beta), the **2.60** refers to the architecture, the **2.60.40** refers to the actual fold (topology) the domain adopts and **2.60.40.720** is the homologous superfamily code. In this example, the CATH code for the domain 1tsrB00 is 2.60.40.720. The **2** refers to the class to which the domain belongs (mainly beta), the **2.60** refers to the architecture, the **2.60.40** refers to the actual fold (topology) the domain adopts and **2.60.40.720** is the homologous superfamily code.
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 The box below shows a 3D structural superposition between the two domains 2pmaA01 and 2rspA00 displayed using the program [[http://jmol.sourceforge.net/|Jmol]].  What you see initially is a wireframe representation of the superposition, which isn't very clear for this purpose, but if you press the grey button labeled **Click here**, the two domains will be coloured differently and the wireframe representation will be replaced by a cartoon representation of the structures, making it much easier to compare them. 2pmaA01 is the blue structure and 2rspA00 the red. The box below shows a 3D structural superposition between the two domains 2pmaA01 and 2rspA00 displayed using the program [[http://jmol.sourceforge.net/|Jmol]].  What you see initially is a wireframe representation of the superposition, which isn't very clear for this purpose, but if you press the grey button labeled **Click here**, the two domains will be coloured differently and the wireframe representation will be replaced by a cartoon representation of the structures, making it much easier to compare them. 2pmaA01 is the blue structure and 2rspA00 the red.
  
-<jsmol :playground:2pmaa012rspa00.pdb.gz 400 400>+<jmol :playground:2pmaa012rspa00.pdb.gz 400 400>
 jmolButton( "cartoon on; cpk off; wireframe off; select *A; color blue; select *B; color red ", "Click here" ); jmolButton( "cartoon on; cpk off; wireframe off; select *A; color blue; select *B; color red ", "Click here" );
-</jsmol>+</jmol>
  
 You can move the structures around by moving the mouse when within the box while holding down the left hand button, and you can zoom in and out by moving the mouse forward and back while holding down the middle button (or track ball). If you press the right hand button on the mouse when in the box, a menu will pop up; please feel free to explore the structures further by selecting the various options. You can always reset the superposition to its initial state by refreshing your browser. You can move the structures around by moving the mouse when within the box while holding down the left hand button, and you can zoom in and out by moving the mouse forward and back while holding down the middle button (or track ball). If you press the right hand button on the mouse when in the box, a menu will pop up; please feel free to explore the structures further by selecting the various options. You can always reset the superposition to its initial state by refreshing your browser.
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 Now, you are going to use Gene3D to explore the HUP superfamily. Please click [[http://gene3d.biochem.ucl.ac.uk/|here]] to go to the Gene3D website.  Now, you are going to use Gene3D to explore the HUP superfamily. Please click [[http://gene3d.biochem.ucl.ac.uk/|here]] to go to the Gene3D website. 
 From the front page go to the "Get superfamily summary" tab and enter the hups superfamily code 3.40.50.620 and click the "Get Superfamily" button. From the front page go to the "Get superfamily summary" tab and enter the hups superfamily code 3.40.50.620 and click the "Get Superfamily" button.
-Which will take you to the a page showing a summary of this superfamily in Gene3D, click [[http://gene3d.biochem.ucl.ac.uk/search?sterm=3.40.50.620&mode=family|here]] to go directly to this page.+Which will take you to the a page showing a summary of this superfamily in Gene3D, click [[http://gene3d.biochem.ucl.ac.uk/superfamily?accession=hups(3.40.50.620)|here]] to go directly to this page.
  
  
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 </box> </box>
  
-CATH has an in-house structural comparison algorithm called SSAP. SSAP takes two structures and calculates how similar they are in structure, residue-by-residue. Similarity is measured by the SSAP score. this ranges from 0 to 100; a score of 100 would indicate that the two structures were effectively identical. Please click [[http://v3-4.cathdb.info/cgi-bin/SsapServer.pl|here]] to go to the SSAP server page. Type in 1aj6A00 as Structure 1 and 1a4hA00 as Structure 2. Press continue. A page will be displayed as follows:+CATH has an in-house structural comparison algorithm called SSAP. SSAP takes two structures and calculates how similar they are in structure, residue-by-residue. Similarity is measured by the SSAP score. this ranges from 0 to 100; a score of 100 would indicate that the two structures were effectively identical. Please click [[http://www.cathdb.info/cgi-bin/SsapServer.pl|here]] to go to the SSAP server page. Type in 1aj6A00 as Structure 1 and 1a4hA00 as Structure 2. Press continue. A page will be displayed as follows:
  
 {{:tutorials:ssap.png|}} {{:tutorials:ssap.png|}}

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