Structure Comparison and Alignment at CE Combinatorial Extension Server

The 3D protein structure comparison and alignment can be performed online using the combinatorial extension algorithm (Shindyalov and Bourrne, 1998) at CE server (Shindyalov and Bourne, 2001). On the CE home page (http://cl.sdsc.edu/ce.html), click All or Representatives PDB, then enter PDB ID into the Specify protein chain box to search for structural alignments from the CE database. From the hit list, select desired entries from the check boxes for sequence alignment and select Neighbors to display the structure neighbors superimposing with the protein specified by the query PDB ID.

To perform sequence alignment and structure comparison,

• Click Two Chains to upload two PDB IDs (e.g., user's query pdb file against PDB file supplied by the user or retrieved form the CE database) on the CE home page.

• On the query form, enter the template PDB ID (either from the CE database or from user's directory) for Chain 1 and enter/browse the query pdb file for Chain 2.

Figure 15.9. Superimposition of 3D protein structures at CE server. The opening graphic window for the superimposition of the modeled (homology modeling with SPDBV) pigeon lysozyme (USR2 in pink) and hen's egg-white lysozyme, ILYZ.pdb (USR1 in blue). The superimposed structures are displayed with the alignment summary (e.g., sequence identity, rms deviation).

Figure 15.9. Superimposition of 3D protein structures at CE server. The opening graphic window for the superimposition of the modeled (homology modeling with SPDBV) pigeon lysozyme (USR2 in pink) and hen's egg-white lysozyme, ILYZ.pdb (USR1 in blue). The superimposed structures are displayed with the alignment summary (e.g., sequence identity, rms deviation).

• Click the Calculate Alignment button to receive Structure Alignment result showing sequence alignment of USR1 (template PDB) and USR2 (query PDB), which can be downloaded as a pdb file.

• Click the Press to Start Compare 3D button to open the display window showing the overlapped structures (Figure 15.9). The menu bar consists of Command (Reset, Exit), Feature table (Browse features...), Align_menu (Control penal), and 3D_menu (rotate, translate, zoom, switch Ca/all atoms).

• Select Feature table ^Browse features ^-Structure or Sequence to analyze the superimposed structures. For example, choosing Structure (Phys)-Secondary structure illustrate secondary structural features of the superimposed structures and choosing Structure (Comp)-Difference displays the structural differences between the superimposed structures as shown in Figure 15.10.

To perform sequence alignment/structure comparison of a query pdb file against the CE database,

• Click Uploaded by the user against the PDB to upload the query pdb file.

• Enter the e-mail address and click the Search Database button. The search and analysis results are returned by the e-mail if the submission is followed by

I—iw I J ■ .- .r---I IQspii^-.S. J ■■ .t \ ■■ ■ ■

Figure 15.10. Structural comparison of the superimposed structures. Structural differences between the superimposed muscle isozyme (3LDH.pdb) and heart isozyme (5LDH.pdb) of lactate dehydrogenase analyzed by the CE server.

I—iw I J ■ .- .r---I IQspii^-.S. J ■■ .t \ ■■ ■ ■

Figure 15.10. Structural comparison of the superimposed structures. Structural differences between the superimposed muscle isozyme (3LDH.pdb) and heart isozyme (5LDH.pdb) of lactate dehydrogenase analyzed by the CE server.

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