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 ...
Gray, Alasdair +4 more
core +7 more sources
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 +4 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
Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family. [PDF]
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
doaj +2 more sources
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
Yumeng Liu, Bin Liu, Xiaolong Wang
core +3 more sources
Prediction of folding patterns for intrinsic disordered protein
Scientific Reports, 2023 The conformation flexibility of natural protein causes both complexity and difficulty to understand the relationship between structure and function. The prediction of intrinsically disordered protein primarily is focusing on to disclose the regions with ...
Jiaan Yang +4 more
doaj +2 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
doaj +2 more sources
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
doaj +2 more sources
Structural and functional studies of intrinsically disordered fibronectin-binding proteins [PDF]
, 2009 Bacterial fibronectin-binding proteins (FnBPs) mediate adhesion of bacteria to host tissues through binding to the human protein fibronectin (Fn). FnBPs are predicted to contain a series of intrinsically disordered Fn-binding repeats (FnBRs), which ...
Norris, Nicole Catherine
core +6 more sources
idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R
PLoS ONE, 2022 Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are proteins or protein-domains that do not have a single native structure, rather, they are a class of flexible peptides that can rapidly adopt multiple conformations ...
William M. McFadden, Judith L. Yanowitz
doaj +3 more sources