Intrinsically disordered proteins and intrinsically disordered protein regions.

By Christopher J. Oldfield, A. Keith Dunker. Annual Review of Biochemistry, 2014

953 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f5b132bc223881cb1d9d13f6eda8c3d54bf94b51

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

APOD: accurate sequence-based predictor of disordered flexible linkers (2020, background): “Specific examples include peptide aggregation (Shvadchak and Subramaniam, 2014), connecting multiple disordered protein binding regions (Oldfield and Dunker, 2014), movement of structured domains between catalytic sites (Anand and Mohanty, 2012), and allosteric regulation (Sorensen and Kjaergaard, 2”
FuzDB: database of fuzzy complexes, a tool to develop stochastic structure-function relationships for protein complexes and higher-order assemblies (2016, background): “Intrinsically disordered proteins (IDPs) or protein regions (IDRs) are abundant in eukaryotic organisms and are known to serve versatile biological roles (1,2).”
DeepCNF-D: Predicting Protein Order/Disorder Regions by Weighted Deep Convolutional Neural Fields (2015, methodology): “Evolutionary information such as PSSM (position specific scoring matrix) generated by PSI-BLAST [2] have been widely accepted to efficiently enhance prediction performance [49].”
Disorder Prediction Methods, Their Applicability to Different Protein Targets and Their Usefulness for Guiding Experimental Studies (2015, methodology): “SAXS is often combined with NMR to provide a more thorough analysis, when NMR fails to give an acceptable overall size and shape estimate [24].”
Transcription factors activate genes through the phase separation capacity of their activation domains (2018, background): “Many of these features have been described for IDRs that are capable of forming phase-separated condensates (Babu, 2016; Darling et al., 2018; Das et al., 2015; Dunker et al., 2015; Habchi et al., 2014; van der Lee et al., 2014; Oldfield and Dunker, 2014; Uversky, 2017; Wright and Dyson, 2015).”
RaptorX-Property: a web server for protein structure property prediction (2016, background): “Sequences in FASTA format can be submitted through the text box or a file (3).”
Unexpected features of the dark proteome (2015, background): “Long known to confound structure determination (15)—thus forming part of the dark proteome—disorder was largely ignored until recently (16) and yet is now known to play key functional roles, especially in eukaryotes (17).”
Protein Phase Separation: A New Phase in Cell Biology (2018, background): “, disorder) and are known as intrinsically disordered proteins/regions (IDPs/IDRs) [37].”
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields (2016, background): “A strong tendency has been observed that disordered regions tend to exist in the coiled state (Becker et al., 2013) and expose to solvent (Oldfield and Dunker, 2014).”
Principles of protein structural ensemble determination. (2017, background): “The importance of using structural ensembles is particularly evident in the case of disordered proteins, which are a class of proteins that lack well-defined structures and instead populate a large number of conformationally heterogeneous states [7,8 ,9 ,10,11].”
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell (2019, background): “323 to evolve, function, and exist as independent, disordered domains [15,65,66].”
AUC-Maximized Deep Convolutional Neural Fields for Protein Sequence Labeling (2016, background): “The solvent accessibility is important for protein folding [10], the order/ disorder state plays an important role in many biological processes [37], and protein secondary structure(SS) relates to local backbone conformation of a protein sequence [38].”
Intrinsically Disordered Proteins and Their “Mysterious” (Meta)Physics (2019, background): “Many IDPs/IDPRs serve as morphing shape-changers that are able to differently fold as a result of binding to different partners [56, 87, 135, 142–144], with the binding region of such a morphing IDP adopting completely different structures in the rigidified assemblies formed by the binding to diverg”
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences (2016, neutral): “A few recent examples include formation of amyloid fibrils (Shvadchak and Subramaniam, 2014), linking multiple disordered protein binding regions (Oldfield and Dunker, 2014), and movement of structured domains between catalytic sites (Anand and Mohanty, 2012).”