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Intrinsically Disordered Proteins

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SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.

Genomics, proteomics & bioinformatics
Intrinsically disordered or unstructured proteins (or regions in proteins) have been found to be important in a wide range of biological functions and implicated in many diseases. Due to the high cost and low efficiency of experimental determination ...

Predicting Protein-Protein Interaction Sites Using Sequence Descriptors and Site Propensity of Neighboring Amino Acids.

International journal of molecular sciences
Information about the interface sites of Protein-Protein Interactions (PPIs) is useful for many biological research works. However, despite the advancement of experimental techniques, the identification of PPI sites still remains as a challenging tas...

Predicting MoRFs in protein sequences using HMM profiles.

BMC bioinformatics
BACKGROUND: Intrinsically Disordered Proteins (IDPs) lack an ordered three-dimensional structure and are enriched in various biological processes. The Molecular Recognition Features (MoRFs) are functional regions within IDPs that undergo a disorder-t...

MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

Journal of theoretical biology
MOTIVATION: Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that p...

The Thermodynamic Basis of the Fuzzy Interaction of an Intrinsically Disordered Protein.

Angewandte Chemie (International ed. in English)
Many intrinsically disordered proteins (IDP) that fold upon binding retain conformational heterogeneity in IDP-target complexes. The thermodynamics of such fuzzy interactions is poorly understood. Herein we introduce a thermodynamic framework, based ...

Decision-Tree Based Meta-Strategy Improved Accuracy of Disorder Prediction and Identified Novel Disordered Residues Inside Binding Motifs.

International journal of molecular sciences
Using computational techniques to identify intrinsically disordered residues is practical and effective in biological studies. Therefore, designing novel high-accuracy strategies is always preferable when existing strategies have a lot of room for im...

Identifying short disorder-to-order binding regions in disordered proteins with a deep convolutional neural network method.

Journal of bioinformatics and computational biology
Molecular recognition features (MoRFs) are key functional regions of intrinsically disordered proteins (IDPs), which play important roles in the molecular interaction network of cells and are implicated in many serious human diseases. Identifying MoR...

Sequence-Based Prediction of Fuzzy Protein Interactions.

Journal of molecular biology
It is becoming increasingly recognised that disordered proteins may be fuzzy, in that they can exhibit a wide variety of binding modes. In addition to the well-known process of folding upon binding (disorder-to-order transition), many examples are em...

cnnAlpha: Protein disordered regions prediction by reduced amino acid alphabets and convolutional neural networks.

Proteins
Intrinsically disordered regions (IDR) play an important role in key biological processes and are closely related to human diseases. IDRs have great potential to serve as targets for drug discovery, most notably in disordered binding regions. Accurat...

IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions.

Bioinformatics (Oxford, England)
MOTIVATION: Despite of the lack of folded structure, intrinsically disordered regions (IDRs) of proteins play versatile roles in various biological processes, and many nonsynonymous single nucleotide variants (nsSNVs) in IDRs are associated with huma...