RING - Residue Interaction Network Generator

Output

The output page of the RING server is divided in two parts. The bottom of the output page shows a summary of the main execution steps performed by the program with the list of interactions found for each of the types.
At the top of the page there are links to various files and pages made by the server:

• Input parameters.

• Network Files for CYTOSCAPE.

• The PDB file corrected by REDUCE (only if Replace all or Keep existing was chosen or if the network is defined by van der Waals contacts).

• The whole code transcript of the RING session.

• The multiple sequence alignment filtered according to the node degree viewed in JALVIEW (only if Node degree sequence alignment was selected).

• Summary of the node degrees (only if Node degree sequence alignment was selected).

• The multiple sequence alignment used to compute residue conservation viewed in JALVIEW (only if Conservation was selected).

Input parameters

This page lists all the input parameters selected by the user. At the top there is part of the PDB file header selected, its code and the selected chain.
The bottom lists the RING parameters entered and selected options for building the interactions network.

PDB file corrected by REDUCE

As previously explained, the isolated -OH, -SH, -NH₃⁺, and Met methyl groups are rotationally optimized by REDUCE. The final rotation angle and score for the best conformation are reported. Optimized H atoms are added to the PDB file.

For each residue, the program accumulates its best score for its clique. For Asn, Gln and His REDUCE also accumulates the best total clique score found for their opposite flip state.

Those scores and the best assignment are written in the output PDB file header. The H atoms of the chosen clique conformation are added to the coordinates field of the output PDB file. Each Asn/Gln/His (unless fixed in advance by a covalent modification) is assigned to one of 4 categories: Keep (K), Flip (F), double-Clash (C), or unknown (X).

For more information on how to read the information added by REDUCE read the reference.

Clicking on the link "PDB" the user can download the PDB file modified by REDUCE.

• If the user has entered a valid PDB file this file will have the corresponding 4 letters PDB code as name with the prefix H_ and the extension .pdb.

• Instead, if the user has loaded a PDB file this file is named H_1ABC.pdb.

Transcript of the RING session

Jalview view of the multiple sequence alignment filtered according to the nodes degree

The button Alignment displays the multiple sequence alignment filtered according to increasing degree of the corresponding nodes directly in JALVIEW. This is the same multiple sequence alignment included in the archive "Network Files for CYTOSCAPE" link (see Cytoscape files description).

The alignment is colored according to ClustalX color scheme. Each sequence contains the field Protein description (DE) which shows the degree threshold under which the sequence has been filtered. This field is displayed in JALVIEW by positioning the pointer over the sequence name.

As mentioned earlier amino acids with higher degree within the interaction network are those more conserved in the multiple sequence alignment.

Summary of the node degrees

This link leads to the page showing information about the node degrees in the interaction network. This contains the same information as the file included in "Network Files for Cytoscape" link (see Cytoscape files description).
The displayed information is:

• The number of contacts for each residue in the sequence.

• Number of residues with exactly grade = n with n growing progressively in the range [1, degree maximum].

• List of residues with exactly grade = n with n growing progressively in the range [1, degree maximum].

• Number of residues with grade ≥ n with n growing progressively in the range [1, degree maximum].

• The higher-degree found in network.

• The identity of residues with maximum degree.

View Jalview conservation multiple sequence alignment:

The button Alignment displays the multiple sequence alignment used to compute residue conservation directly in JALVIEW. This contains the same information as node attribute file describeded in "Node Files for CYTOSCAPE" link (see Cytoscape files description).

The alignment is colored according to ClustalX color scheme. .

As mentioned earlier amino acids with high conservation play an important role in the function and structure of proteins.