Required - Job name: you must input a valid job name in the text box labeled as "Job name". A valid job name can not have any space(s) and/or special characters except dash (-) and underscore (_). The job name should be between 4 and 10 characters long. Outputs will be generated based on your provided job name.

Required - protein model: you must provide a valid protein model for the scoring. You can either copy and paste the model in the textarea labeled as "Copy and paste a model" or upload the model using the upload button labeled as "Or upload a model". The model must conform to the valid PDB format and the length must be between 10 and 500 residues. Here you may find the information about valid PDB format.

For testing purpose, you may either populate the textarea with an example protein model by clicking the "Example" button located at the top right corner of the textarea or download the "example.pdb" by clicking the "Example" button located at the bottom left corner of the "Choose File" button and subsequently upload the model for processing.

Optional - Email address: although an email address is not required, it is recommended that you provide a valid email address in the field labeled as "Email address" for receiving the job-related update. Your email address will not be public and only be used for communicating the job status.

iQDeep provides a range of options that allows you to calibrate your job by customizing the scoring mode, scoring resolution, and privacy.

Scoring mode: iQDeep offers two different scoring modes, individual mode and batch mode. You may either select individual or batch mode for scoring. However, if you select the batch mode, a new job submission form will appear. You need to input at least 2 valid models and the corresponding amino acid sequence. The sequence must exactly match the sequence in the input models.

Scoring resolution: iQDeep offers scoring of protein models using two different scoring resolutions, "Standard" resolution and "High" resolution with a default set to "Standard" resolution. "Standard" resolution mode performs the scoring by employing multiscale deep residual neural networks (ResNets) trained at the resolutions of standard version of Global Distance Test (GDT-TS) metric. On the other hand, the "High" resolution mode performs the scoring by employing multiscale deep residual neural networks (ResNets) trained at the resolutions of high-accuracy variant of Global Distance Test (GDT-HA) metric.

Privacy: your submitted job and corresponding results will be accessible publicly unless you choose to keep your job private by selecting the checkbox marked as "Keep my job private". If you keep your job private, no user including you, will be able to access the results directly from the job queue. However, you may still limitedly track the progress of your job from the job queue. In such a scenario, you can access the corresponding results only by using the prompted URL at the time of job submission. The URL will also be sent to your valid email address if you provide one. However, if you choose not to provide a valid email address, you should record the job URL from the job submission confirmation window.

iQDeep allows you to track your submitted job status as it is being processed. Keeping your job public enables you to directly track the status from the job queue as well as access the results. Therefore, your job will be clickable from the "Job Queue" panel as shown below,


Currently, "Job Queue" promptly shows one of the following status for a valid job,

Once you click the job name, it will navigate you to the job status page, showing real-time job status as follows,


Additionally, in the "Job parameters" panel, you can see the user-specified "Job parameters".

Once your job has finished processing, you can navigate to the result analysis page by clicking the "Results" button. Meanwhile, you can download the results by clicking the "Download" button.

Tracking a job using the URL

The results page reports the predicted global quality of the input model(s) as shown below for the example results.


The example is processed using the batch mode. The models are sorted based on the predicted global quality. You can select individual model to see detail results for the corresponding model.

Analysis of the structural properties appear just below the predicted global quality panel. It shows the similarity between the predicted and observed secondary structure and solvent accessibility as shown below for the example,


Here the top row represents sequence number based on pose residue numbering. Colon (:) denotes a match between the predicted secondary structure and solvent accessibility of a residue in the model, space (' ') otherwise.

iQDeep provides a three dimensional representation of the scoring model under the "Model" panel for an interactive visualization of the model as shown below,


You can visualize each model by clicking a model from the predicted global quality panel at the left.

In addition to reporting the global quality, iQDeep provides the graphical analysis of the local quality under the "Predicted local quality panel" as shown below,


The local quality shows the predicted error estimates of a residue from the residue in the corresponding native structure.

During the scoring of a model, iQDeep utilizes the interaction between the observed and predicted contact maps at 6, 8, 10, 12, and 14Å. It provides a graphical representation of the corresponding observed and the predicted contact maps at the aforementioned 5 thresholds as shown below,



For a specific threshold, the observed and the predicted contact map is calculated using a sequecne seperation of 5. iQDeep uses DMPfold predicted distance histogram to extract the predicted contact maps. You may find the detail information on calculating the predicted contact map here.