Alternative views

Results page provides viewing of the results target-by-target. Groups view allows assessing performance of a particular prediction group over all the targets predicted by that group. Both the re-compiled tables and graphical results - with predictions from the group in question specially indicated - are available. Table Browser adds the capability to generate custom comparisons of numerical results where prediction groups, targets, and measures may be selected by the user.

Results page

The Results page allows access to (1) 3D interactive representations of the target structures (2) tabulated numerical results (TABLES), (3) GDT plots, (4) alignment quality bar graphs, (5) comparison of models with template structures; and (6) Spice-based interactive target/model/template visualization. Targets may be selected based on prediction category (TBM - template based modeling, FM - template free modeling. See also Categories of prediction).

(1) Target structures

Target structures may be viewed with Rasmol, Chime, or Protein Explorer, as installed on a local workstation. The evaluated areas are colored green. There are two reasons why some areas of the target may not be colored: (a) target was split into domains and only the domain in question is highlighted, and (b) some residues were eliminated from evaluation by the assessors.

(2) TABLES

Models are identified with target and prediction group numbers. Group name and results of the LGA sequence-dependent and sequence-independent analyses, MAMMOTH analysis, and DAL local structure analysis are provided for each model. Text files, interactive renderings of model and target in a sequence dependent and sequence independent superpositions, as well as links to the GDT plots are also provided (links through letters A, D, I, and G respectively). Tables may be sorted according to results in each column and may be expanded or contracted with full/brief options. Additional descriptions (e.g. of measures) are provided through links in the tables.

(3) GDT plots

(3) GDT plots These plots provide analysis of prediction quality by finding the largest subset of residues in the model that can be fitted to the target in a rigid body sequence dependent superposition. This is done for cutoffs ranging from 0.5 to 10.0 Angstroms. Results are plotted as a line for each model separately. Models from several groups may be displayed simultaneously; and conversely, clicking on any line in the plot will identify the corresponding model and research group (dark blue indicates Model 1, cyan - other models submitted by that group).

(4) Alignment quality

The bar graphs indicate percentages of correctly aligned residues in the model relative to target (green), those aligned with an error not larger than 4 residues (yellow), and those aligned with an error of 5 or larger (red). Additional set of bar graphs indicates the distribution of the correctly and incorrectly aligned residues along the target protein sequence. Clicking on each bar produces a 3D interactive rendering of a superimposed model and target in the best rigid body sequence independent superposition (obtained with LGA). Further details and definitions are provided through links in graphs.

(5) Value-added plots

User-selected models are plotted versus target sequence and compared with best templates for that target. Template availability for each residue of the target structure is also indicated. The analysis allows identifying regions where model structure is closer to target than any available template (negative regions of the "difference" graph).

(6) Spice visualization (Java)

Spice (Sanger Institute) visualization tool allows simultaneous viewing of several model structures and/or a corresponding target structure. Users can toggle between three viewing servers (sequence-dependent and sequence-independent LGA modes and a non-rigid body local descriptors viewing mode) selected from the Menu Alignment. Best ten identified templates for the selected target can also be superimposed onto the target/model in the sequence-independent alignment mode (template structures can be found at the bottom of the list). Three panels of the Spice tool are interactively connected, so for example selecting a region in the alignment panel will highlight this region in the 3D panel. Basic Spice functions are quite intuitive and the manual is available through Help.