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tutorials:mali_tutorial [2015/09/16 15:52] – [Exploring Drug Design] hafsatutorials:mali_tutorial [2015/09/22 14:07] (current) – [A Short Introduction to CATH and Gene3D] hafsa
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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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 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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-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|}}
tutorials/mali_tutorial.1442418774.txt.gz · Last modified: by hafsa

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