PreDom Help

DiD (Predict interface)

How to use

1. Select the domain structure database to use in the "Database" cell.
2. Click [Browse...] next to the [PDB format file] field and select the PDB format file of the target data. Then click [Find chains] to list all the chain IDs in the specified data, and select the chain ID from the list.
   To clear the chain list, click [Reset]. (The [PDB format file] field is also initialized.)
3. Modify the value of the following parameters if needed.

   Threshold of sequence identity

   The mininum of the required sequence identity with the target domain of the homologous domains.

   Threshold of sequence coverage

   The minimum of the required sequence coverage by the target domain of the homologous domains.

   Threshold of E-value

   The maximum of the allowed E-value for performing BLAST search.

   Threshold of IP score

   The minimum of the required IP score (score evaluated on the basis of the occurrence of each amino acid residue on the domain-domain interface).

   Threshold of residue contact

   The maximum of the allowed distance between atoms in the candidate domain-domain interface residues. A residue pair is regarded to be in contact with one another when all the distances between atoms of each residue are within this value.

   Minimum size of interface

   The minimum of the required number of contacted residues. Predicted domain-domain interaction residues are discarded when the number of contacted residues among them is less than this value.

4. Click [Start Prediction] to execute prediction.

Description of the result page

List of the results (bottom left table)

List of the obtained results. All the results by the KIP method are listed first, then the results by the IP method follow.

Field name	Description
method	Method of the prediction (KIP or IP)
homologous domain	ID of the homologous domain (only for the results by the KIP method). By clicking the link, the amino acid sequence and the 3D structure of that domain are displayed on another window.
Identity/coverage	The sequence identity/coverage of the homologous domain (only for the results by the KIP method).

Amino acid sequence (top left box)

The amino acid sequence of the target domain. The predicted domain-domain interface residues of the result selected by the leftmost radio button in the result list are indicated with blue-green background color. By placing the mouse pointer over one of the interface residues, the residue name and the residue number are displayed in the "interaction residue" field below.

3D Structure (right box)

The Jmol visualization of the target domain. The predicted domain-domain interface residues are shown in cpk format, while other residues are shown in cartoon format. By placing the mouse pointer over one of the interface residues in the amino acid sequence, the corresponding residue color in this figure turns white to indicate its position in the structure.

Item	Description
[cartoon][cpk] buttons	Buttons to change the display format of the residues except the domain-domain interface residues
[spin] checkbox	Switch to start/stop to spin the structure.

Setting of the definition of interface residues (topmost checkbox)

Select the requirement for the domain-domain interface residues to display.

Checked:

Only the residues whose positions and residue names both coincide with those of the domain-domain interface residues in the homologous domains are displayed as the interface residues.

Unchecked:

All the residues located at the positions of the domain-domain interface residues in the homologous domain are displayed as the interface residues.