The FunFOLD Server Help Page

Input sequence

Enter the amino acid sequence of your target protein here in single letter format e.g.

	MIETPYYLIDKAKLTRNMERIAHVREKSGAKALLALKCFATWSVFDLMRDYMDGTTSSSL
	FEVRLGRERFGKETHAYSVAYGDNEIDEVVSHADKIIFNSISQLERFADKAAGIARGLRL
	NPQVSSSSFDLADPARPFSRLGEWDVPKVERVMDRINGFMIHNNCENKDFGLFDRMLGEI
	EERFGALIARVDWVSLGGGIHFTGDDYPVDAFSARLRAFSDRYGVQIYLEPGEASITKST
	TLEVTVLDTLYNGKNLAIVDSSIEAHMLDLLIYRETAKVLPNEGSHSYMICGKSCLAGDV
	FGEFRFAEELKVGDRISFQDAAGYTMVKKNWFNGVKMPAIAIRELDGSVRTVREFTYADY
	EQSLS
	

Email address

Enter your e-mail address here. Results will be returned as soon as they are available.

Short name for sequence

Use this field to 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 name you specify will be included in the subject line of the e-mail messages sent to you from the server.

Results

Both machine readable and interactive graphical results are provided (Click here for an example of graphical output for CASP9 target T0515). The image shows the top predicted 3D model annotated to indicate putative binding site residues. The cartoon 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) ligand, 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 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.

The format of the email attachment is compatible with the CASP FN format.