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tutorials:mali_tutorial [2015/09/16 15:52] hafsa [Exploring Drug Design] |
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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| 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|}} | ||
