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tutorials:workshop [2017/10/24 09:23] – sayonitutorials:workshop [2019/06/19 15:02] (current) – sillitoe
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 {{ :tutorials:4ig6_uploaded_to_cath.png }} {{ :tutorials:4ig6_uploaded_to_cath.png }}
  
-Each chain of the PDB can be submitted for structural scans separately. Submit **chain A** of the uploaded PDB to the structural scan by clicking on 'Submit Structure' for chain A. If the servers are busy, you might find that the job takes a long time to complete - you can skip the wait and view the previously calculated results **[[http://www.cathdb.info/search/grid_submission/9574|here]]**.+Each chain of the PDB can be submitted for structural scans separately. Submit **chain A** of the uploaded PDB to the structural scan by clicking on 'Submit Structure' for chain A. If the servers are busy, you might find that the job takes a long time to complete - you can skip the wait and view the previously calculated results **[[http://www.cathdb.info/search/grid_submission/12264|here]]**.
  
 A total of 528 matching structures in CATH v4.1 have been found, with scores ranging from very good (in green) through to very poor (in red). A total of 528 matching structures in CATH v4.1 have been found, with scores ranging from very good (in green) through to very poor (in red).
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 Whilst the CATHEDRAL algorithm you used at the beginning of the tutorial is fast and allows you to search all structures in CATH, SSAP is a slower and slightly more accurate method for comparing two protein structures.  Whilst the CATHEDRAL algorithm you used at the beginning of the tutorial is fast and allows you to search all structures in CATH, SSAP is a slower and slightly more accurate method for comparing two protein structures. 
  
-SSAP takes two structures and calculates how similar they are in structure, residue-by-residue. Similarity is measured by the SSAP score. This score ranges from 0 to 100; a score of 100 would indicate that the two structures were effectively identical. Please click **[[http://cath-tools.cathdb.info/pairwise|here]]** to go to the SSAP server page. Type in **1od6A00** as Domain ID 1 and **1f7uA01** as Domain ID 2. Press 'GO'.+SSAP takes two structures and calculates how similar they are in structure, residue-by-residue. Similarity is measured by the SSAP score. This score ranges from 0 to 100; a score of 100 would indicate that the two structures were effectively identical. Please click **[[http://cath-tools.cathdb.info/structure/pairwise|here]]** to go to the SSAP server page. Type in **1od6A00** as Domain ID 1 and **1f7uA01** as Domain ID 2. Press 'GO'.
  
 From this superposition we can see that the two domains are significantly different in structure. This structural divergence is also clearly highlighted by their SSAP score of 58.77 and an RMSD of 8.15Å. From this superposition we can see that the two domains are significantly different in structure. This structural divergence is also clearly highlighted by their SSAP score of 58.77 and an RMSD of 8.15Å.
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 The next thing we can look at is whether or not there are local changes, particularly around the active site, for example, residue mutations in the site and changes in catalytic residues. Taking 1h7oA00 and 1d3gA00 as our examples, we can go back to their respective functional family pages and look at the multiple alignments for those families. Highly conserved residues are highlighted in the alignment (as shown above) and the structure and you can compare them side by side to observe any differences. We are currently in the process of adding in catalytic residue information to the FunFam pages so that conserved residue and catalytic residue information can be viewed on the FunFam MSA and the representative structure. The next thing we can look at is whether or not there are local changes, particularly around the active site, for example, residue mutations in the site and changes in catalytic residues. Taking 1h7oA00 and 1d3gA00 as our examples, we can go back to their respective functional family pages and look at the multiple alignments for those families. Highly conserved residues are highlighted in the alignment (as shown above) and the structure and you can compare them side by side to observe any differences. We are currently in the process of adding in catalytic residue information to the FunFam pages so that conserved residue and catalytic residue information can be viewed on the FunFam MSA and the representative structure.
  
-We can also use SSAP to create a superposition of our two proteins and then compare the position of functional residues. Just type **1h7oA00** as protein 1 and **1d3gA00** as protein 2. An interactive RasMol image of the superimposed structures can be brought up by pressing the **Launch Rasmol** button. Initially, a simple backbone superposition will be displayed but you can change to a cartoon display by typing in **select*** and **cartoon on** in the command console (see picture below) +We can also use [[http://cath-tools.cathdb.info/structure/pairwise|SSAP]] to create a superposition of our two proteins and then compare the position of functional residues. Just type **1h7oA00** as protein 1 and **1d3gA00** as protein 2 and click on ‘GO’. An interactive LiteMol visualization of the superimposed structures in cartoon representations is shown.
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-{{:tutorials:rasmol.png|}}+
  
 +{{:tutorials:ssap_litemol.png|}}
  
 The [[http://www.ebi.ac.uk/thornton-srv/databases/CSA/| Catalytic Site Atlas]] is a database containing enzyme active sites and catalytic residues in enzymes. We want to use this resource to determine the catalytic residues for our aldolase examples and map them onto the RasMol 3D structure. At the top of the homepage, you will find a field labelled **PDB code**. Type in 1h7o and then 1d3g to get a list of catalytic residues for these proteins (see picture below for example) The [[http://www.ebi.ac.uk/thornton-srv/databases/CSA/| Catalytic Site Atlas]] is a database containing enzyme active sites and catalytic residues in enzymes. We want to use this resource to determine the catalytic residues for our aldolase examples and map them onto the RasMol 3D structure. At the top of the homepage, you will find a field labelled **PDB code**. Type in 1h7o and then 1d3g to get a list of catalytic residues for these proteins (see picture below for example)
  
-Once you have your catalytic residues, highlight them on your RasMol superposition using the following commands - **select n1, n2, n3** etc (where n//x// denotes a catalytic residue number, for example, 17) then **spacefill** and then select a color - for example type **colour purple** if you want the catalytic residues for one of the proteins to be purple. +A jmol of the SSAP superposition has been provided with the catalytic residues of the domains highlighted. Here, 1h7oA00 is in pink, with its catalytic residues red and 1d3gA00 light blue with its catalytic residues blue
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-A jmol of the SSAP superposition has been provided in case you have difficulties with the SSAP server. Here, 1h7oA00 is in pink, with its catalytic residues red and 1d3gA00 light blue with its catalytic residues blue+
  
 <jsmol 1h7o_2 :tutorials:1h7oA00_1d3gA00.pdb.gz 80% 400> <jsmol 1h7o_2 :tutorials:1h7oA00_1d3gA00.pdb.gz 80% 400>
tutorials/workshop.1508836987.txt.gz · Last modified: by sayoni

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