Description

This the first panel visible to the user. This panel present the summary of the job submitted by the user.

Z Score Cutoff: This section shows the threshold value of Z score used for the prediction. Since, the Z score can change based on options selected by the user while submitting the job, hence this value can vary across the jobs.

PDB Details:It reports the number of interacting interfaces in the PDB and the number of subunits or chains. Please note that the actual number of interfaces may be more than the reported number as PIZSA will only consider the interacting interfaces. The interacting interfaces are identified based on interacting amino acid residues.

Interface Details: This section shows the aggregate scores for the particular interface and the binding prediction. If there are multiple interfaces then the scores will be reported for all of them. Figure-1 shows the scores for just one interface.

Color Legend: This section shows the coloring legend for the different chains of the PDB structure. This is helpful in identifying specific residues and to distinguish the chains.

Description

This panel reports all the details about the selected interface. For multimers, user need to select from the drop down menu the specific interface to see its details.

Parameter Scores: This section shows the result in a columnar table format. User can also see the definition and formulation of a given parameter by clicking on the parameter name.

Download the results: User can also download the displayed data in a tab separated file by clicking the 'Download Scores File' button (present on the top right hand side corner of the panel).

Description

This panel shows the interacting residues between the selected interface.

The results sorted by the 'Raw Score' column 'Interface residue One' show the residue form the first interface and the 'Interface Residue Two' shows the residues from the second interface.

Searching the entries: User can search table entries containing specific residue name, chain or residue number. For searching, just type in the keyword in the search box (on the top right hand side of the panel.)

Sorting the results: The table entries can also be sorted by any column. For example the results can be sorted by residue number (increasing or decreasing order), residue name or chain. For sorting, just click on the column label's.

Visualization: This panel is integrated with the Jsmol molecular viewer. User can highlight the residue of interest by hovering the cursor on the specific table row which will highlight the specific residue pair in the Jsmol viewer.

Download the results: User can also download the displayed data in a tab separated file by clicking the 'Download Interacting Residues File' button (present on the top right hand side corner of the panel).

Description

This panel shows the results of mutational analysis (if the option was selected while submitting the job).

The results sorted by the 'Score-Diff' column.

Searching the entries: User can search table entries containing specific residue name, chain or residue number. For searching, just type in the keyword in the search box (on the top right hand side of the panel.)

Visualization: This panel is integrated with the Jsmol molecular viewer. User can highlight the residue of interest by hovering the cursor on the specific table row which will highlight the specific residue in the Jsmol viewer.

Download the results: User can also download the displayed data in a tab separated file by clicking the 'Download Mutational Analysis File' button (present on the top right hand side corner of the panel).

Description

This panel displays the 3D structure of the PDB submitted by the user.This panel is automatically linked with the 'Interacting Interface Residues panel and Mutational Analysis Panel'.

Using JSmol options: User only need to right-click inside the visualization panel to enable various JSmol controls.