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Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins [PDF]
, 2020 The need for accurate and efficient force fields for modeling 3D structures of macrobiomolecules and in particular intrinsically disordered proteins (IDPs) has increased with recent findings to associate IDPs and human diseases.
Liu, Hao +4 more
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Frontiers in Molecular Biosciences, 2015 Intrinsically Disordered Proteins (IDPs), or protein fragments also called Intrinsically Disordered Regions (IDRs), display high flexibility as the result of their amino acid composition. They can adopt multiple roles.
Gabriel eThieulin-Pardo +3 more
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CARs-DB: A Database of Cryptic Amyloidogenic Regions in Intrinsically Disordered Proteins
Frontiers in Molecular Biosciences, 2022 Proteome-wide analyses suggest that most globular proteins contain at least one amyloidogenic region, whereas these aggregation-prone segments are thought to be underrepresented in intrinsically disordered proteins (IDPs).
Carlos Pintado-Grima +7 more
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IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields [PDF]
International Journal of Molecular Sciences, 2018 Accurate prediction of intrinsically disordered proteins/regions is one of the most important tasks in bioinformatics, and some computational predictors have been proposed to solve this problem. How to efficiently incorporate the sequence-order effect is critical for constructing an accurate predictor because disordered region distributions show global
Yumeng Liu, Xiaolong Wang, Bin Liu
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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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Open questions: Reflections on intrinsically disordered proteins [PDF]
Network Biology, 2021 Intrinsically Disordered Proteins or Regions (IDPs) are proteins that lack a predetermined 3D structure playing key cellular functions including regulation, signaling, and protein-protein/DNA interaction.
Mouna Choura, Ahmed Rebai
doaj
Journal of Chemical Theory and Computation, 2023 Intrinsically disordered proteins (IDPs) populate a range of conformations that are best described by a heterogeneous ensemble. Grouping an IDP ensemble into “structurally similar” clusters for visualization, interpretation, and analysis purposes is a ...
Rajeswari Appadurai +4 more
semanticscholar +1 more source
Order, Disorder, and Everything in Between
Molecules, 2016 In addition to the “traditional” proteins characterized by the unique crystal-like structures needed for unique functions, it is increasingly recognized that many proteins or protein regions (collectively known as intrinsically disordered proteins (IDPs)
Shelly DeForte, Vladimir N. Uversky
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A novel mode of interaction between intrinsically disordered proteins
Biophysics and Physicobiology, 2020 An increasing number of proteins, which have neither regular secondary nor well-defined tertiary structures, have been found to be present in cells. The structure of these proteins is highly flexible and disordered under physiological (native) conditions,
Emi Hibino, Masaru Hoshino
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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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