Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources

By Marcin J. Mizianty, Wojciech Stach, Ke Chen, Kanaka Durga Kedarisetti, Fatemeh Miri Disfani, Lukasz Kurgan. 2010

176 citations recorded by the source corpus.

Motivation: Intrinsically disordered proteins play a crucial role in numerous regulatory processes. Their abundance and ubiquity combined with a relatively low quantity of their annotations motivate research toward the development of computational models that predict disordered regions from protein sequences. Although the prediction quality of these methods continues to rise, novel and improved predictors are urgently needed. Results: We propose a novel method, named MFDp (Multilayered Fusion-based Disorder predictor), that aims to improve over the current disorder predictors. MFDp is as an ensemble of 3 Support Vector Machines specialized for the prediction of short, long and generic disordered regions. It combines three complementary disorder predictors, sequence, sequence profiles, predicted secondary structure, solvent accessibility, backbone dihedral torsion angles, residue flexibility and B-factors. Our method utilizes a custom-designed set of features that are based on raw predictions and aggregated raw values and recognizes various types of disorder. The MFDp is compared at the residue level on two datasets against eight recent disorder predictors and top-performing methods from the most recent CASP8 experiment. In spite of using training chains with ≤25% similarity to the test sequences, our method consistently and significantly outperforms the other methods based on the MCC index. The MFDp outperforms modern disorder predictors for the binary disorder assignment and provides competitive real-valued predictions. The MFDp's outputs are also shown to outperform the other methods in the identification of proteins with long disordered regions. Availability: http://biomine.ece.ualberta.ca/MFDp.html Supplementary information: Supplementary data are available at Bioinformatics online. Contact: lkurgan@ece.ualberta.ca

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Improving protein disorder prediction by deep bidirectional long short‐term memory recurrent neural networks (2016, methodology): “For example, SVMs have been utilized in MFDp (Mizianty et al. , 2010), POODLE L and S (Hirose et al. , 2007; Shimizu et al. , 2007), PrDOS (Ishida and Kinoshita, 2007), Spritz (Vullo et al. , 2006) and with an RBF kernel in the most recently released model, Dispredict (Iqbal and Hoque, 2014).”
Genome‐scale prediction of proteins with long intrinsically disordered regions (2014, background): “Since the chains in the MxD set are characterized by pairwise sequence identity below 25%,43 the TRAINING and TEST datasets also share this low level of similarity.”
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins (2012, background): “For example the MFDp meta-predictor [50] can be installed locally, but it depends on more than ten third-party programs (e.”
Comprehensive review of methods for prediction of intrinsic disorder and its molecular functions (2017, methodology): “MFDp 2010 [64] WS Yes (up to 5) http://biomine.”