Basic Enviroment

When the application is executed the following interface is shown:

ProtDCal main window

Table 1: Main screen details

Name Description
A Menu Summary of commands for execution
B Toolbar Frequently used commands.
C Panels The indices, groups and aggregation_operator implemented in ProtDCal.

The panels below the toolbar represent the three of the hierarchical levels described above (Modification Operators are accessed via the Options menu). When you mouse over each element, a brief text description pops up explaining its functionality. Panels (indices, groups and aggregation operators) are subdivided, according to their nature, into several subpanels.

Indices Panel

The panel of indices is divided into four subpanels (Thermodynamic Indices for Structures, Thermodynamic Indices for Sequences, Topographic Indices, and Properties-based Indices).

Indices Panel

In the Topographic Indices subpanel, there are several weighted indices (starting with the letter "w"), that can be calculated using one or several weights for inter-residue contacts. The following figure shows the window intended for selecting the properties to be used as weights for contacts. This window appears every time one of these weighted indices is selected, in such a way that different properties can be selected for different indices. Alternatively, if many indices will use the same weighting properties, one could first select all the topographic indices at once by clicking the button 'Topographic Indices of Folded Protein States', which launches the properties window once, and then the user may deselect the non-desired indices. These indices will be identified in the outputs as follows: "index_name(weight)".

Weight Window

Other indices can be computed using "TAE Aminoacid Descriptor..." and "Other Indices..." buttons located at the end of the panel. The first option, calculates Transferable Atom Equivalent (TAE) indices available in: http://reccr.chem.rpi.edu/Software/Protein-Recon/TAE.doc..

The second option computes defined properties (see Creating new Properties)using the "Define new indices" option located in the menu "Option/Manage Indices". This options display the following window:

Select Indices Window

In this window the (), (ALL) and () buttons can select the indices previously defined.

Groups Panel

In the panel of groups there are three subpanels enclosing groups by residue ID, properties and topographic features. Also with the "Others groups..." button is possible to select groups previously defined by the user (see Define new groups).

Groups Panel

Aggregation_Operator Panel

The panel of aggregation operators is divided into four categories: distances, central tendency, dispersion and information theoretic metrics. In the central tendencies subpanel, specifically for harmonic and geometric means, there are three implemented variants to evaluate these metrics in order to avoid possible in definitions associated with '0' values:

Aggregation_Operator Panel