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DALI output describes the following :
'''Profunc'''


''Z score'' , the statistical significance of the similarity between protein-of-interest and other neighbourhood protines. The program optimises a weighted sum of similarities of intramolecular distances.
''Related protein sequences''
[[Image:profunc2.jpg|framed|none]]


''Root Mean Square Distance (RMSD)'', root-mean-square deviation of C-alpha atoms in the least-squares superimposition of the structurally equivalent C-alpha atoms. As in indicated in DALI, rmsd is not optimised and is only reported for information.
''Proteins with similar fold retrived from SSM (Secondary Structure Matching)''


''lali'', the number of structurally equivalent residues.  
[[Image:ssm2.jpg|framed|none]]


''nres'', or the total number of amino acids in the hit protein.  
From Profunc, similarities of related proteins and proteins with similar fold to query protein were compared with results from DALI. 2qgnA is the query protein highlighted in black in all tables. 2crm, 2crr and 2crq were both found in DALI and Profunc(highlighted in red). On the other hand, 2ze5,2ze6,2ze7 and 2ze8, as well as 3adk and 2qor were also found in DALI output(highlighted in blue).  
 
''%id'' - percentage of identical amino acids over structurally equivalent residues.


[[Profunc Results|Next]]
[[Profunc Results|Next]]

Revision as of 06:03, 10 June 2008

Structural Alignment

Dali Output

PDB entry code for 2qgn was loaded onto DALI server to search for structurally similar neighbours. Displayed below are the results from DALI search :-

Dali output3.jpg


Profunc

Related protein sequences

Profunc2.jpg

Proteins with similar fold retrived from SSM (Secondary Structure Matching)

Ssm2.jpg

From Profunc, similarities of related proteins and proteins with similar fold to query protein were compared with results from DALI. 2qgnA is the query protein highlighted in black in all tables. 2crm, 2crr and 2crq were both found in DALI and Profunc(highlighted in red). On the other hand, 2ze5,2ze6,2ze7 and 2ze8, as well as 3adk and 2qor were also found in DALI output(highlighted in blue).

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