Developed by Alan R. Mól, Wagner Fontes, Mariana S. Castro.
Laboratório de Bioquímica e Química de Proteínas (LBQP) - Universidade de Brasília - Brazil
This application is available free of charge. If you would like to cite it, please use the following reference:
For quick examples of styles and also one-click changes, check the 'Styles' tab. Advanced ajustments, as well as other features, are available using the other tabs, explained below:
This tab is used to set the parameters of the polygons used to represent each amino acid residue in both projections. The options are all available by group, and a pretty straightforward.
The Pattern tab is only meaningful for circles, and is used to add lines to them, which can be specially useful for black and white images.
Colors are set using hexadecimal codes, which can be easily created from the color picker. This is also valid for every other color option used in the application.
The Size parameter defines the size of the biggest polygon of the projection. The ratio between the size of first and the last polygon is defined by the First/Last Ratio. Thus, a First/Last Ratio of 0.1 means that the the first polygon will have approximately 10% of the area of the last one, and a Ratio of 2 will lead to the first polygon being twice as big as the last.
The Labels are the characters printed on top or around the polygons with information regarding which amino acid it represents.
Labels can be set in different styles, including combinations of the peptide position and code. One useful feature is the ability to add an offset to the position counter. By default, the positions start at 1, but this can be changed in order to use the real positiong regarding the whole peptide or protein sequence.
Two tabs are available here. The Amino acids tab can be considered a primary tab, with all labels styles available. If separate display of the residues and the position is desired, this can be achived by using the Position tab.
The Guides tab sets the lines used to illustrate the order in which the residues are displayed on the projection, and also the possible frame around the figure.
The order guides work differently on the Net and Wheel projections. On the Net projection, they follow the residues order in the given peptide. On the Wheel projection, this is accomplished by the Connection Lines (Wheel tab), and the guides represent the order following the circle order. In this case, they are useful when a Spiral Factor greater than 0 is used, to maintain the round characteristic.
This tab has options to enable/disable the legend, set the labels (useful in case different grouping is used, translations or other preferences) and the legend's position. The Aesthetics tab can be used to specify the font-size and also some advanced parameters regarding the representation of circle patterns on the legend, if necessary.
Note that only groups found in the Sequence will be shown on the legend.
The groups tab can be used to change how amino acids are divided into 5 different groups. It's primary features are on the default tab Residues.
The default approach considers all residues inside one of the 4 groups according to polarity and acidity, and one extra group for unknown residues. This can be changed, however, as needed. For instance, it can be considered that Glycine is a special case, given it's minimum side-chain, instead of a nonpolar residue. This can't be used simultaneously with a Unkown Residue group, however.
Note that all characters used in the sequence MUST be located in one of the 5 groups, or the projection will not be generated. Whitespaces, albeit discouraged, are allowed.
This tab also allows the definitions of possible interactions between residues, which are one of the main features of the Net projection. Nonpolar and hydrogen-bonding residues interact with residues of the same type, while Acid/Basic residues will interact with each other. Again, this can be used for different meanings, as long as the interactions pairs are maintained (Nonpolar/nonpolar, H/H, Acid/Basic).
On the second tab, Labels, it's possible to change the Groups labels displayed on the User Interface. This does not affects the projections (unless the new labels are copied to the legends, but this can be changed idenpendently on the Legend tab), but can be helpful if the groups in use are different from the default, and the different names make everything too confusing.
A title can be added to both projections, but it's rather limited in terms of length and color.
Positioning on the wheel projection is rather easy, but not so much on the Net projection, since its size varies according to the number of residues.
The position of the title can be adjusted using the x and y inputs, separated for each projection. For the Net projection, the Auto Adjust Position will try to position the title automatically at the top of the image, while also updating the image heigth.
Both title and image positions can be adjusted if needed to better fit the title. The title position can be adjusted in the relative positioning fields and the images position can be adjusted in the respective padding fields, under the Net or Wheel tabs.
This tab offers options specific to the Net projection.
The buttons allow for easy switch between common helices, but all they do is change the Residues per turn value. The x-axis position of the first amino acid will vary according to the number of residues, but it can be ajusted using the Start Offset input.
The Show Border option adds a vertical line indicating the position along the central helix axis where the cut was done for the projection. This can be very illustrative if Padding Left or Paddign Right is greater than 0, otherwise it might look like there are more residues than on reality.
Changes to the paddings will cause the polygons to have non proportional dimensions. If that's the case, the Proportion Factor input can be adjusted to make them look good again.
This options are esclusive of the Wheel projection.
Connection Lines are the lines that go from one polygon to the other, following the peptide sequence. These lines can have their width and gray range adjusted.
The Spiral Factor determines if every polygon should be a little closer to the center of the circle than the one before it, organizing them over a spiral, instead of a circle. The Nesting Factor regards the distance between circles (or spirals) if more residues than 18 (or Period) are present.
Other parameters ajust the properties related to the physicochemical characteristics of the helix.
The Figure Size group of parameters is important when it's necessary to change the size of the image following changes to the Legend and the addition of a Title.
This tab offers buttons to change some parameters quickly at once, without having to change multiple values.
For example, all polygons shape can be changed to Circles, or the Label Style considering all possibilites.
The Tools tab currently has only one tool, which is exporting the current parameters to a text file that can be locally stored by the user. This allows you to load the parameters used once to create a new projection with the same design, or maybe just change a couple of details.
Unfortunately, this option can be very sensitive to updates, specially if a parameter is removed (probably split). Yet, we try not to change too much in order to maitain backwards compatibility.
The Exporting feature is one of the main advantages of the NetWheels application. Even though you can simply right-click the image and save it, this feature allows you to export the projection in high quality, with high resolution, to different formats.
The PDF format can be edited on software with read this type of file, like Adobe's Photoshop and Illustrator.