The FunFOLD2 Server Help Page
This page contains simple guidelines for using the new version of the FunFOLD server, sample input data which may be downloaded and submitted and an example of output from the server.Guidelines for using the server
The FunFOLD server version 2.0 only requires you to enter the amino acid sequence of your target protein. Other input fields are optional. If you also decide to provide your email address then you will be sent a link to the graphical results and machine readable results when your predictions are completed. However, if you do not provide your email address then you must bookmark the results page and so that you may refer to the results when they become available.Input sequence
Paste or enter the amino acid sequence of your target protein in the text box using the single letter amino acid code e.g.
Sample sequence:
MGEILAVDDYVGISFWLAAAIMLASTVFFFVERSDVPVKWKTSLTVAGLVTGVAFWHYLY MRGVWIYAGETPTVFRYIDWLITVPLQIIEFYLIIAAVTAISSAVFWKLLIASLVMLIGG FIGEAGLGDVVVWWIVGMIAWLYIIYEIFLGETAKANAGSGNAASQQAFNTIKWIVTVGW AIYPIGYAWGYFGDGLNEDALNIVYNLADLINKAAFGLAIWAAAMKDKETSTSHA
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.
Optional - Short name for sequence
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 FunFOLD 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.
Example of output from the server
The results page shows the top predicted 3D model annotated to indicate putative binding site residues. The ribbon view of the model is shown in green and the binding site resides are shown as blue sticks with labelled residues. The view is zoomed and centred on the first (N-term) binding residue. A link is provided for downloading a PDB file of the top model with all identified ligands superposed in their likely positions relative to the model.
Below the download link is a list of the binding residues is provided along with the most likely (numerous) ligands, the ligand identified at nearest to the centre of the predicted binding pocket and a list of the likely interacting ligands and the number of each that were identified in related template structures.
The Jmol view follows and it provides numerous options for viewing the ligand binding site prediction. In the default view, for clarity, the binding site residues are shown as sticks and the labels and ligands are switched off.
After the Jmol view is a list of quality assessment scores provided by FunFOLDQA method and the per-residue propenisty scores in CAMEO LB format.
If you provide your email address, then file attachments are also provided, which are compatible with the CASP FN format and CAMEO LB format.