TopDomain Documentation Page

Submitting a Job

The job will be available for 7 days after the calculations are finished. After that, it will be deleted. User entered data will not be shared with any third parties.

Email

Entering an email address is optional. If you provide an email address, a link to the results webpage will be send to that email. Your email address will not be shared with any third parties.

Giving a Job Name

An optional job name can be set. The downloadable results archive will then have the job name as an identifier. The job name must not be longer than 30 characters and may only consist of letters, numbers, and the underscore ('_') symbol.

Input

TopDomain predicts protein domain boundaries. This prediction can be based on an input structure (See File Upload section) or an input amino acid sequence using both sequence and template information (TopDomain) or only using sequence information (TopDomain_Seq). Entering DNA or RNA sequences, or non-standard amino acid letters, will not be accepted by the server. The length of the entered sequence must be between 50 and 2000 residues. The server will only accept single sequences. If you want to model multiple proteins, please enter the sequences separately.

File Upload

TopDomain can predict domain boundaries based on an input structure (TopDomain_Parse). When running TopDomain on an input structure, the uploaded file must be in .pdb format. The maximum length of a .pdb file is 2000 residues.

Example Run

If you want to try out the server, two example runs are prepared. Example 1 presents the results of running the sequence mode, whereas example 2 presents the results of a structural mode job. Both examples use the pyruvate kinase protein from rabbit (PDB ID: 1AQF).

Interpreting the Results

Requirement of domain parsing

If the input is a sequence, the first prediction is if cutting the target sequence into domain is a necessary step for protein structure prediction or if there are templates available that are predicted to cover all domains in the right relative domain orientation. This prediction is based on TopDomain_TMC (see the TopDomain paper for an in-depth description). If domain parsing is considered to not be required, the top five templates that are predicted to have proper domain coverage and orientation are reported.

Sequence-based Prediction

The sequence-based prediction is calculated by TopDomain_Seq (see the TopDomain paper for an in-depth description). It is a sequence-based prediction of protein domain boundaries. The prediction is displayed as a boundary-score plot with detected peaks showing the location of the predicted boundaries as blue vertical lines. The 68% confidence interval of each boundary prediction is predicted from the peak height and indicated as a green shaded area in the plot.

Homology-based Prediction

The homology-based prediction is calculated by TopDomain (see the TopDomain paper for an in-depth description). It is a sequence- and template-based prediction of protein domain boundaries. The prediction is displayed as a boundary-score plot with detected peaks showing the location of the predicted boundaries as blue vertical lines. The 68% confidence interval of each boundary prediction is predicted from the peak height and indicated as a green shaded area in the plot.

Structure-based Prediction

The structure-based prediction is calculated by TopDomain_Parse (see the TopDomain paper for an in-depth description). It is a structure-based prediction of protein domain boundaries. The prediction is displayed as a boundary-score plot with detected peaks showing the location of the predicted boundaries as blue vertical lines. The 68% confidence interval of each boundary prediction is predicted from the peak height and indicated as a green shaded area in the plot.

Support

If you have any questions or suggestions, please write an email to cpcweb[at]uni-duesseldorf.de.

Literature