The FunFOLD2 server for the prediction of protein–ligand interactions

By Daniel B. Roche, Maria T. Buenavista, Liam J. McGuffin. 2013

50 citations recorded by the source corpus.

The FunFOLD2 server is a new independent server that integrates our novel protein–ligand binding site and quality assessment protocols for the prediction of protein function (FN) from sequence via structure. Our guiding principles were, first, to provide a simple unified resource to make our function prediction software easily accessible to all via a simple web interface and, second, to produce integrated output for predictions that can be easily interpreted. The server provides a clean web interface so that results can be viewed on a single page and interpreted by non-experts at a glance. The output for the prediction is an image of the top predicted tertiary structure annotated to indicate putative ligand-binding site residues. The results page also includes a list of the most likely binding site residues and the types of predicted ligands and their frequencies in similar structures. The protein–ligand interactions can also be interactively visualized in 3D using the Jmol plug-in. The raw machine readable data are provided for developers, which comply with the Critical Assessment of Techniques for Protein Structure Prediction data standards for FN predictions. The FunFOLD2 webserver is freely available to all at the following web site: http://www.reading.ac.uk/bioinf/FunFOLD/FunFOLD_form_2_0.html.

Subfields: Computational Theory and Mathematics, Molecular Biology

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Citations in the corpus

IntFOLD: an integrated web resource for high performance protein structure and function prediction (2019, methodology): “The IntFOLD server provides a single point of access to an integrated suite of six component methods: IntFOLD-TS, for tertiary structure prediction (9–11,18,19); ModFOLD, for 3D model Accuracy Self-Estimate (ASE) scoring (9,20); ReFOLD, for 3D model refinement (9,21); DISOclust, for disorder predict”
IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences (2015, methodology): “The method has since been updated to include a range of new binding site quality estimates (25) as well as per-atom P-values for ligand contacts in CAMEO-LB format (4).”