tutorials:structural_functional_analysis
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| tutorials:structural_functional_analysis [2015/09/14 13:10] – [Eukaryotic Hexokinases] hafsa | tutorials:structural_functional_analysis [2015/09/21 15:05] (current) – [The CATHEDRAL Server] hafsa | ||
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| ==== The CATHEDRAL Server ==== | ==== The CATHEDRAL Server ==== | ||
| - | First of all, you need to retrieve all the domains present in FtsA. You can use the CATHEDRAL server to do this. The CATHEDRAL server employs a structural comparison algorithm to compare the query structure against known domains in the CATH database, which means you can also use it to try and identify a unknown protein by comparing it with all known structures in CATH. You submit the protein for analysis at [[http://beta.cathdb.info/ | + | First of all, you need to retrieve all the domains present in FtsA. You can use the CATHEDRAL server to do this. The CATHEDRAL server employs a structural comparison algorithm to compare the query structure against known domains in the CATH database, which means you can also use it to try and identify a unknown protein by comparing it with all known structures in CATH. You submit the protein for analysis at [[http://v3-4.cathdb.info/ |
| <box Info|''' | <box Info|''' | ||
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| - | To find the domain in CATH, enter the domain code (i.e. 1e4f followed by the chain ID and domain ID) into the search box [[http://www.cathdb.info|on the CATH website]] and look at the result. If you look at the homologous superfamily level (the H-level) you will see that the domain has the code 3.30.420.40. Click on this level to view the structures of other known domains from this homologous superfamily. | + | To find the domain in CATH, enter the domain code (i.e. 1e4f followed by the chain ID and domain ID) into the search box [[http://update.cathdb.info/|Click Here]] and look at the result. If you look at the homologous superfamily level (the H-level) you will see that the domain has the code 3.30.420.40. Click on this level to view the structures of other known domains from this homologous superfamily. |
| <box Question|Question> | <box Question|Question> | ||
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| For this family you are going to look at interactions. For this you are going to start with the Actin-related protein (arp) with the PDB code 1k8kA. Search this term in the Gene3D | For this family you are going to look at interactions. For this you are going to start with the Actin-related protein (arp) with the PDB code 1k8kA. Search this term in the Gene3D | ||
| - | (or follow this shortcut [[http:// | + | (or follow this shortcut [[http:// |
| <box Question|Question> | <box Question|Question> | ||
tutorials/structural_functional_analysis.1442236235.txt.gz · Last modified: by hafsa
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