XdomView tutorial page

The objective of  the program is to provide graphical visualization of domain regions in protein 3D structures and the intron-exon boundary regions in homologous protein sequences.


This tutorial explains the features of Xdom using the PDB code:1HKB and chain: A as input query. 
(Click on the images below to view enlarged version)

1 - Query Input

  • In the query page, enter 1HKB in the PDB code field. 

  • Enter A in the chainID field.

  • For this example, the default e-value is retained (1e-10).

  • Click 'submit' button.

 

2 - Result Output

The output consists of 5 sub-windows - PDB code viewer, Domain viewer, Gap viewer, Intron position viewer and Structure viewer, as shown in the figure.

 

 

 

 

 PDB code viewer 

Displays the PDB code and the chains.

 Domain viewer 

Displays the protein domain regions as defined in CATH, SCOP, DALI, NCBI, 3DEE.

 Blast gap viewer

Displays the Blast alignment gaps between the input PDB chain sequence and the ExInt protein sequences.

 Intron position viewer

Displays the intron positions and phase in the ExInt protein sequence.

 PDB structure viewer

Displays backbone structure of the input PDB chain.
 

3 - Domain Viewer

  1. Clicking on a database name in the Domain viewer window displays the corresponding domain definitions of the structure in the PDB structure viewer window (link 1 and 4). 
  2. For example, clicking on CATH (link 1) displays domains for chain A of 1HKB based on CATH domain classification.
  3. Clicking on the differentially-coloured segments in the Domain viewer window highlights the corresponding domain regions in the structure (link 2 and 3).
 

 

4 - Intron Position viewer and Blast Gap viewer

1. Clicking on the ExInt ID of the aligned sequence (link 1), results in mapping of the exons in the sequence to the protein structure displayed in the structure viewer. The Blast gap viewer window also gets activated, as shown in the figure. In this case, gaps are absent in the alignment.

2. Link 2 displays exon regions for a different ExInt ID. The alignment gaps due to insertion or deletion are shown in various colours.

3. Link 4 maps the alignment gaps to the protein structure in the PDB structure viewer as shown in the figure. For clearer visualization of gaps, the image can be enlarged by holding down the 'SHIFT' key while moving the mouse.

4. The red box (link 5) provides the BLAST alignment for the specified ExInt ID against the sequence of 1HKB in text format. 

For any comments or suggestions, contact vivek@bic.nus.edu.sg