The ModFOLDdock server help page

This page contains simple guidelines for using the new version of the ModFOLDdock server, sample input data which may be downloaded and submitted and examples of output from the server.

Guidelines for using the server

The only required input for using the ModFOLDdock server is the amino acid sequence for your target protein.

If you wish, you may also provide your email address, which will only be used to provide you with a link to the results when your predictions are completed. However, if you do not provide your email address then you should bookmark the results page so you can view the results when they are available.

Required - Input sequences of protein target (FASTA format)

In the text box labelled "Input sequences of protein target" please carefully paste in the full amino acid sequence/s for your target assembly in FASTA format. Sequences for an example multimer target (CASP15 target H1151) are below:

Sample sequences:

>H1151 P9WF37, Mycobacterium tuberculosis, subunit 1, 112 residues;
MAHHHHHHVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYG
VTRERIRQIESKTMSKLRHPSRSQVLRDYLDGSSGSGTPEERLLRAIFGEKA
>H1151 P9WF37, Mycobacterium tuberculosis, subunit 2, 116 residues;
MRYAFAAEATTCNAFWRNVDMTVTALYEVPLGVCTQDPDRWTTTPDDEAKTLCRACPRRW
LCARDAVESAGAEGLWAGVVIPESGRARAFALGQLRSLAERNGYPVRDHRVSAQSA
	

Required - Stochiometry

If you know the stoichiometry of your assembly, please include it here, because you will get more accurate models. For example the target H1151 above, is a heterodimer with stoichiometry: A1B1.

A monomer=A1, a homodimer=A2, a homotrimer=A3, a homotetramer=A4, and so on. A heterodimer=A1B1, a heterotrimer=A1B1C1, a heterotetramer=A1B1C1D1, and so on.

You can also model targets with more complex stoichiometries, such as a dimer of dimers=A2B2, a trimer and dimer=A3B2, a nonamer and trimer=A9B3, and so on. You must provide a sequence for each subunit in your complex.

Required - Model Data

Using the file selector labelled "Upload model/models" you may either upload a single PDB file (to obtain quality predictions for a single model), or multiple PDB files (to obtain quality predictions for many alternative models) in the form of a tarball (a tarred and gzipped directory).

Please ensure that each separate PDB file contains the coordinates for one model only. Please do not upload a single PDB file containing the coordinates for multiple alternative models. The coordinates for multiple models should always be uploaded as a tarred and gzipped directory of separate files.

The server will attempt to automatically renumber the ATOM records in each model in order to match the residue positions in the sequence i.e. the coordinates for the first residue in the sequence will be renumbered "1" in each model file (if they aren't already), the coordinates for the second residue in the sequence will be numbered "2", and so on.

Important note concerning incomplete models: If your model files contain many missing residues, e.g., models for discontinuous domains, then you will either need to provide the full length sequences, or you will need to renumber the ATOM records, so that the residues are sequential in accordance with the partial sequence. Please note that if you submit the full length sequence and there are a high number of missing residue coordinates in your models, then these will count against the models in the global scoring. In this case, the global scores may be more appropriate if you submit the partial sequences along with your correctly numbered model files, i.e., with sequential numbering of residue coordinates.

Sample PDB file:
An example file containing a single model for the sample sequence shown above can be downloaded below:

Example of model built for CASP15 target H1151: H1151TS180_1.pdb

Sample Tarball file:
The tarball should contain a directory of separate PDB files for your target sequence. This file should be similar in format to the tarballs of 3D models found on the CASP website.
An example tarball file containing multiple models for the sample sequence shown above can be downloaded below:

Tarball of multiple server models for CASP15 target H1151: H1151.tar.gz

Steps to produce a tarball file for your own 3D models:
Linux/OSX/other Unix

1. Tar up the directory containing your PDB files e.g. type the following at the command line: tar cvf my_models.tar my_models/
2. Gzip the tar file e.g. gzip my_models.tar
3. Upload the gzipped tar file (e.g. my_models.tar.gz) to the ModFOLD server

Windows users
In Windows you can use a free application such as 7-zip to tar and gzip your models.

1. Download, install and run 7-zip
2. Select the directory (folder) of model files to add to the .tar file, click "Add", select the "tar" option as the "Archive format:" and save the file as something memorable e.g. my_models.tar
3. Select the tar file, click "Add" and then select the "GZip" option as the "Archive format:" - the file should then be saved as my_models.tar.gz
4. Upload the the gzipped tar file (e.g. my_models.tar.gz) to the ModFOLD server

Optional - Short name for protein target

If you wish, you may assign a short memorable name to your prediction job. This is useful so that you can identify particular jobs in your mailbox. This is particularly important because ModFOLDdock will not necessarily return your results in the order you submitted them. The set of characters you can use for the filename are restricted to letters A-Z (either case), the numbers 0-9 and the following other characters: .~_- The name you specify will be included in the subject line of the e-mail messages sent to you from the server.

Optional - E-mail address

If you wish, you may provide your e-mail address. You will be sent a link to the graphical results and machine readable results when your predictions are completed.

Privacy Notice: Processing of personal data will be in accordance with the GDPR and University of Reading (UoR) Data Protection Policy. Users' IP addresses will be temporarily stored in the queuing system and then used to generate anonymous usage statistics. Optionally, users may provide an email address, so that they can be notified when their job completes; this will be deleted when no longer required. Personal data will be accessible only by UoR staff managing the server, and will not be stored for longer than is necessary for the provision of the service. Your results will be available via a unique URL, which will not be posted publicly. Your sequences and structures will not be used for any other purposes and will deleted after the expiry date (21-28 days).

Output from the server

The ModFOLDdock server produces a results page with a table containing numerical prediction results with buttons to view models interactively in 3D with different colouring options. The raw machine readable prediction data is also provided in CASP QA format

Examples of output:

1. ModFOLDdock results for CASP15 target T1132 (A6)
2. ModFOLDdockR results for CASP15 target H1106 (A1B1)
3. ModFOLDdockS results for CASP15 target T1173 (A3)
4. ModFOLDdock results for CASP15 target H1151 (A1B1)

Description of output:

The results table is ranked according to the predicted global assembly and interface quality scores. The global model quality scores range between 0 and 1. In general scores less than ~0.5 indicate there may be incorrectly modelled subunits and scores greater than 0.5 generally indicate more complete and confidently assembled models, which are highly similar to the native structure.

Each row in the table also provides buttons for colouring models either by chain identifier or predicted local interface quality, and for downloading models as PDB files. The local quality colouring relates the confidence scores for all interface residues in the model, ranging from dark blue (high confidence of the residue being in the interface), through lighter blues, whites and yellows (lower confidence), to red (very low confidence, or non-interface residue). A button is also provided to download a PDB file of the model with residue accuracy predictions in the B-factor column.
(The results page is based on the code from: https://wwwuser.gwdg.de/~mmirdit/casp15/?code=1).

Browser compatibility:

Linux: Chrome, Firefox
MacOS: Firefox, Chrome, Safari
Windows: Chrome, Edge, Firefox

Fair usage policy:

You are only permitted to have 1 job running at a time for each IP address, so please wait until your previous job completes before submitting further data. If you already have a job running then you will be notified and your uploaded files will be deleted. Once your job has completed your IP address will be unlocked and you will be able to submit new data.

If you wish to submit numerous sequences or batch jobs then please contact l.j.mcguffin@reading.ac.uk, with a short description of your project.