Structure comparison

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It is a good idea to familiarise yourself with your structure by giving first a description (you will find examples how to do this in many papers concerned with protein structures). However, before you do so I recommend to first compare the structure to all known structures (described below). If there are similar structures, then you can look up their architectural classification in the SCOP database and it will help you to define the architecture of your proteins. Give the protein fold (c.f. SCOP), known domains (c.f. InterPro) and potentially a schematic representation of the organisation of secondary structure elements.

Even if your protein is not related by sequence to any known protein structure (check this!) it is possible that similar structures are known. To actually compare your structure to other known structures you can use either the CE or the Dali web server.

Read the results carefully! How great is the structural similarity (accuracy)? How significant is that similarity (significance)? How much of the structure is similar (coverage)? What is the sequence identity between the structural similar proteins, and what residues are identical (these may be important for the function!!)?

--ThomasHuber 16:46, 25 April 2007 (EST)