Flexible Structural Neighborhood - workflow

FATCAT Home Pairwise Alignment Database Searching Structural Neighbors References Help
Step 1: input either a PDB code or a SCOP code
This figure shows the home of the Flexible Structural Neighborhood. When you click on the "Structure Neighbors" in the FATCAT homepage, you will get here.
Step 2: the protein summary page for a PDB protein (this step is skiped if input of step 1 is SCOP code)

This page shows all chains and domains(if available) for a given PDB protein identified by its PDB code. The complex chains are shown graphically. but for chains with low complexity, non-protein chains or chains with no domain defined by SCOP, only their sequences are available. The following is 2 two examples(one for a PDB protein classified by SCOP, the other one is not).

This PDB protein(1e2w) has been processed by SCOP. It has 2 chains(A and B) and they are identical (with same uniq_id as shown in the chain bar). Each of the chain has 2 domains. Segments with same colors are different segments of a single domain(d1e2wa1).
This PDB protein(1te1) has NOT been processed by SCOP. It has 2 chains(A and B).

Chain A is not calculated directly by our server because the structure neighborhood of its representative protein (1om0A) has been calculated. In fact, "1te1A" is identical to "1om0A" in sequence as shown in the subfigure (the box in the lower right coner). It's the sequence alignment between "1te1A" and "1om0A" when one clicks on "1te1 chain A"(the green arrow) Because the representative protein(1om0A) has been processed by SCOP, its structure neighborhood is calculated in domain level. One should click on its domains(the light blue arrow) to see their structure homologs.

However, chain B(1te1B) was calculated directly and it has no homologs(at 90% Id level) with PDB proteins annotated by SCOP. One should click on the chain itself(the red arrow) to find out its structure neighborhood.

Step 3: the structure neighborhood page when one clicks on either a domain or a chain in Step 2.
This example shows a list of structures found in SCOP167_90, which are similiar to protein d1e2wa1 (assume the user clicked on "d1e2wa1" in Step 2, B1). The subfigure (D) is the graphic view of twist frequency along the query protein "d1e2wa1" as it aligns to the current list of structure homologs. As we can see this family of proteins has one region which is more flexible than other parts of the protein. Moreover, one can change the alignment parameters(as shown in top of the page) to customize the structure homlog list. Also the results are downloadable.

NOTE: Sometime this page is not exactly the result of your submitted query, instead it shows the result of another protein, which is homologous to your query( ≥90% sequence identity, 100% identitical in many cases), because only a representive set is calculated directly. If this is case for your query, the page will display a warning message on the top of the page. Also the sequence alignment between your query and its representative is available. If you really want the result for your query instead of its representative, you can go to our live Database Searching page but it will take a few hours to calculate the structure alignments.

Step 4: the individual structural alignment between the query and any one of the structure homologs
This page will assist users to look into the details of a individual structural alignment.
  • the strucuture alignment corresponding to their sequences.
  • view and download the graph of FATCAT chaining results
  • view the 3D structure superpostion by Chime Plug-in
  • download superposed PDBs and rasmol scripts

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Current support provided by
NIH grant GM101457 - Development of the Flexible Comparative Modeling Toolkit

Previous supports provided by
NSF grant DBI-0349600, NIH grant GM63208 and NIH grant GM076221