Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins
Biomolecules, 2019 Intrinsically disordered proteins (IDP) are abundant in the human genome and have recently emerged as major therapeutic targets for various diseases. Unlike traditional proteins that adopt a definitive structure, IDPs in free solution are disordered and ...
Supriyo Bhattacharya, Xingcheng Lin
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RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins [PDF]
Briefings in Bioinformatics, 2020 AbstractAs an important type of proteins, intrinsically disordered proteins/regions (IDPs/IDRs) are related to many crucial biological functions. Accurate prediction of IDPs/IDRs is beneficial to the prediction of protein structures and functions. Most of the existing methods ignore the fully ordered proteins without IDRs during training and test ...
Yumeng Liu, Xiaolong Wang, Bin Liu
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Scientific Reports, 2017 Intrinsically disordaered proteins (IDPs) are a prevalent phenomenon with over 30% of human proteins estimated to have long disordered regions. Computational methods are widely used to study IDPs, however, nearly all treat disorder in a binary fashion ...
Tomasz Kosciolek +2 more
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Evolutionarily conserved network properties of intrinsically disordered proteins. [PDF]
PLoS ONE, 2015 Intrinsically disordered proteins (IDPs) lack a stable tertiary structure in isolation. Remarkably, however, a substantial portion of IDPs undergo disorder-to-order transitions upon binding to their cognate partners.
Nivedita Rangarajan +2 more
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The IDP-Specific Force Field ff14IDPSFF Improves the Conformer Sampling of Intrinsically Disordered Proteins [PDF]
Journal of Chemical Information and Modeling, 2017 Intrinsically disordered proteins (IDPs) or intrinsically disordered regions do not have a fixed tertiary structure but play key roles in signal regulation, molecule recognition, and drug targeting. However, it is difficult to study the structure and function of IDPs by traditional experimental methods because of their diverse conformations ...
Dong Song, Ray Luo 0001, Hai-Feng Chen
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The lifestyle switch protein Bd0108 of Bdellovibrio bacteriovorus is an intrinsically disordered protein. [PDF]
PLoS ONE, 2014 Bdellovibrio bacteriovorus is a δ-proteobacterium that preys upon Salmonella spp., E. coli, and other Gram-negative bacteria. Bdellovibrio can grow axenically (host-independent, HI, rare and mutation-driven) or subsist via a predatory lifecycle (host ...
Gerd Prehna +2 more
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Intrinsically Disordered Proteins and the Janus Challenge
Biomolecules, 2018 To gain a new insight into the role of proteins in the origin of life on Earth, we present the Janus Challenge: identify an intrinsically disordered protein (IDP), naturally occurring or synthetic, that has catalytic activity.
Prakash Kulkarni, Vladimir N. Uversky
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Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and molecular dynamics study. [PDF]
PLoS Computational Biology, 2012 The unique ability of intrinsically disordered proteins (IDPs) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks.
Iskra Staneva +3 more
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Regulated Disorder: Posttranslational Modifications Control the RIN4 Plant Immune Signaling Hub
Molecular Plant-Microbe Interactions, 2019 RIN4 is an intensively studied immune regulator in Arabidopsis and is involved in perception of microbial features outside and bacterial effectors inside plant cells.
Tania Y. Toruño +3 more
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An Evolutionary Algorithm for the Design of Different Degrees of Secondary Structure in Intrinsically Disordered Proteins (IDPs) [PDF]
Biophysical Journal, 2015 In recent experimental studies of coupled folding and binding of IDPs investigators have adapted methods from the protein folding literature whereby point mutations are used to identify the degree to which different regions are pre-folded prior to the rate limiting step in binding and folding. These approaches assume a one-to-one correspondence between
Harmon, Tyler S., Pappu, Rohit V.
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