The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

Abstract

The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

The mysterious presence of a 5-methylcytosine oxidase in theDrosophilagenome

“…Models were based on the template 3s57 chain a of the human aBH2 protein and were built and evaluated using the intFOLD, i-tassEr and ModFOLD4 servers and the sParKs-x and Modeler standalone programs. [73][74][75][76] Details of the modeling approach are provided in the Supplementary Material. the images of models were rendered using PyMOL.…”

Phytophthora infestans RXLR Effector PexRD2 Interacts with Host MAPKKKε to Suppress Plant Immune Signaling

“…Originally identified in P. infestans isolate 88069, PexRD2 is a member of Tribe 6, an 18-member RXLR effector family in P. infestans (Haas et al, 2009). Members of this family are predicted, at least in part, to adopt the same WYdomain fold, and some of this family can be modeled on the PexRD2 structure with high confidence scores using IntFOLD (Roche et al, 2011). As such, we predict that this family may have evolved as interaction modules, potentially targeting host proteins of similar structure and function.…”

In Silico Identification of Prioritized Interacting Domains in Primary Immunodeficiency Disease Causing Genes

“…The obtained data clearly demonstrates that more functional annotation of domains in disease causing genes can be identified through such in silico analysis. To check this hypothesis, we used domain prediction using context (DPUC) [31] and DomFOLD [32] tools. These tools provide computationally predicted domains for given protein sequences.…”