The MultiFOLD server help page

This page contains simple guidelines for using the new version of the MultiFOLD 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 MultiFOLD 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 (CASP16 target H1202) are below:

Sample sequences:

>H1202 Q9GZX9_plus_P43026, Human, subunit 1, 69 residues;
ETGCNKALCASDVSKCLIQELCQCRPGEGNCSCCKECMLCLGALWDECCDCVGMCNPRNY
SGTLEVLFQ
>H1202 Q9GZX9_plus_P43026, Human, subunit 2, 121 residues;
MAPLATRQGKRPSKNLKARCSRKALHVNFKDMGWDDWIIAPLEYEAFHCEGLCEFPLRSH
LEPTNHAVIQTLMNSMDPESTPPTCCVPTRLSPISILFIDSANNVVYKQYEDMVVESCGC
R
	

Optional - Stochiometry

If you know the stoichiometry of your assembly, please include it here, because you may get more accurate models.

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.

For example the target H1202 above, is a heteromer with stoichiometry: A2B2.

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 MultiFOLD 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 MultiFOLD 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 TS format

Examples of output:

1. MultiFOLD2 results for CASP16 target H1202 (A2B2 stoichiometry provided)
2. MultiFOLD2 results for CASP16 target T0206 (A2 stoichiometry correctly predicted)
3. MultiFOLD2 results for CASP16 target H0232 (A2B2 stoichiometry correctly predicted)
4. MultiFOLD2 results for CASP16 target T0240 (A3 stoichiometry correctly predicted)

Description of output:

The results table is ranked according to decreasing global predicted model quality score (plDDT and pTM). The global model quality scores range between 0 and 1. In general scores less than ~0.5 indicate there may be incorrectly modelled domains and scores greater than 0.5 generally indicate more complete and confident models, which are highly similar to the native structure.

Each row in the table also provides 3 buttons that display the model interactively with colouring by chain identifier or local quality. The local quality colouring ranges from blue (accurate) to red (inaccurate). A button is also provided to download a PDB file of the model with residue accuracy predictions in the B-factor column.
(The result page code is adapted 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.