IDP-LM: Prediction of protein intrinsic disorder and disorder functions based on language models.
PLoS Computational Biology, 2023 Intrinsically disordered proteins (IDPs) and regions (IDRs) are a class of functionally important proteins and regions that lack stable three-dimensional structures under the native physiologic conditions.
Yihe Pang, Bin Liu
doaj +3 more sources
AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins [PDF]
The Journal of Physical Chemistry B, 2018 The associative memory, water-mediated, structure and energy model (AWSEM) has been successfully used to study protein folding, binding, and aggregation problems.
Peter G. Wolynes (46354) +2 more
core +3 more sources
Creating and Exploiting the Intrinsically Disordered Protein Knowledge Graph (IDP-KG) [PDF]
, 2022 There are many data sources containing overlapping information about Intrinsically Disordered Proteins (IDP). IDPcentral aims to be a registry to aid the discovery of data about proteins known to be intrinsically disordered by aggregating the content ...
Mičetić, Ivan +6 more
core +4 more sources
Modeling disordered protein interactions from biophysical principles.
PLoS Computational Biology, 2017 Disordered protein-protein interactions (PPIs), those involving a folded protein and an intrinsically disordered protein (IDP), are prevalent in the cell, including important signaling and regulatory pathways.
Lenna X Peterson +4 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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Martini3-IDP: improved Martini 3 force field for disordered proteins
Nature CommunicationsCoarse-grained (CG) molecular dynamics (MD) is widely used for the efficient simulation of intrinsically disordered proteins (IDPs). The Martini model, one of the most popular CG force fields in biomolecular simulation, was reported to yield too compact ...
Liguo Wang +4 more
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How multisite phosphorylation impacts the conformations of intrinsically disordered proteins.
PLoS Computational Biology, 2021 Phosphorylation of intrinsically disordered proteins (IDPs) can produce changes in structural and dynamical properties and thereby mediate critical biological functions.
Fan Jin, Frauke Gräter
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Predictions of Backbone Dynamics in Intrinsically Disordered Proteins Using De Novo Fragment-Based Protein Structure Predictions [PDF]
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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PLoS Computational Biology, 2013 Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions.
Jianhui Song +4 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.
Luo, Ray +5 more
core +6 more sources