On the public citation graph

Effects of Sequence Composition and Patterning on the Structure and Dynamics of Intrinsically Disordered Proteins

https://doi.org/10.1101/2020.06.08.137752
0 signed · 97 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.
Claim with ORCID
Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.
See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/elps.200800673openalex-snapshot
Modeling the separation of macromolecules: A review of current computer simulation methods
inferredcites →https://doi.org/10.1002/jcc.21005openalex-snapshot
ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions
inferredcites →https://doi.org/10.1002/pro.2261openalex-snapshot
A decade and a half of protein intrinsic disorder: Biology still waits for physics
inferredcites →https://doi.org/10.1007/978-94-007-5464-5_1openalex-snapshot
Towards a Coarse-Grained Model for Unfolded Proteins
inferredcites →https://doi.org/10.1016/0022-2836(76)90004-8openalex-snapshot
A simplified representation of protein conformations for rapid simulation of protein folding
inferredcites →https://doi.org/10.1016/0079-6107(72)90005-3openalex-snapshot
Protein volume in solution
inferredcites →https://doi.org/10.1016/b978-012267351-1/50005-5openalex-snapshot
Monte Carlo Simulations
inferredcites →https://doi.org/10.1016/j.bbapap.2012.12.008openalex-snapshot
Unusual biophysics of intrinsically disordered proteins
inferredcites →https://doi.org/10.1016/j.bbapap.2017.06.008openalex-snapshot
Insights into the conformations and dynamics of intrinsically disordered proteins using single-molecule fluorescence
inferredcites →https://doi.org/10.1016/j.biocel.2011.04.001openalex-snapshot
Intrinsically disordered proteins from A to Z
inferredcites →https://doi.org/10.1016/j.bpj.2010.02.006openalex-snapshot
Sequence Determinants of Compaction in Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1016/j.bpj.2010.12.278openalex-snapshot
Charge Interactions Can Dominate the Dimensions of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1016/j.bpj.2014.07.060openalex-snapshot
Probing the Disordered Domain of the Nuclear Pore Complex through Coarse-Grained Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1016/j.bpj.2014.07.071openalex-snapshot
Modest Influence of FRET Chromophores on the Properties of Unfolded Proteins
inferredcites →https://doi.org/10.1016/j.bpj.2017.04.021openalex-snapshot
Phase Separation and Single-Chain Compactness of Charged Disordered Proteins Are Strongly Correlated
inferredcites →https://doi.org/10.1016/j.bpj.2019.02.028openalex-snapshot
The Role of Cohesiveness in the Permeability of the Spatial Assemblies of FG Nucleoporins
inferredcites →https://doi.org/10.1016/j.febslet.2004.09.036openalex-snapshot
Reduced amino acid alphabet is sufficient to accurately recognize intrinsically disordered protein
inferredcites →https://doi.org/10.1016/j.jmb.2012.01.016openalex-snapshot
Small-Angle X-ray Scattering and Single-Molecule FRET Spectroscopy Produce Highly Divergent Views of the Low-Denaturant Unfolded State
inferredcites →https://doi.org/10.1016/j.sbi.2015.03.008openalex-snapshot
Relating sequence encoded information to form and function of intrinsically disordered proteins
inferredcites →https://doi.org/10.1016/j.sbi.2017.01.006openalex-snapshot
Computational and theoretical advances in studies of intrinsically disordered proteins
inferredcites →https://doi.org/10.1016/j.tibs.2012.08.004openalex-snapshot
Intrinsically disordered proteins: a 10-year recap
inferredcites →https://doi.org/10.1016/s0079-6107(01)00012-8openalex-snapshot
Predicting properties of intrinsically unstructured proteins
inferredcites →https://doi.org/10.1017/jfm.2013.668openalex-snapshot
Rotne–Prager–Yamakawa approximation for different-sized particles in application to macromolecular bead models
inferredcites →https://doi.org/10.1021/acs.chemrev.6b00163openalex-snapshot
Coarse-Grained Protein Models and Their Applications
inferredcites →https://doi.org/10.1021/acs.jctc.5b00736openalex-snapshot
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
inferredcites →https://doi.org/10.1021/acs.jctc.7b00143openalex-snapshot
Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1021/acs.jpcb.5b09133openalex-snapshot
An Adequate Account of Excluded Volume Is Necessary To Infer Compactness and Asphericity of Disordered Proteins by Förster Resonance Energy Transfer
inferredcites →https://doi.org/10.1021/bi00327a032openalex-snapshot
Theory for the folding and stability of globular proteins
inferredcites →https://doi.org/10.1021/cr400514hopenalex-snapshot
Introducing Protein Intrinsic Disorder
inferredcites →https://doi.org/10.1021/cr400525mopenalex-snapshot
Classification of Intrinsically Disordered Regions and Proteins
inferredcites →https://doi.org/10.1021/ja503069kopenalex-snapshot
Concerted Dihedral Rotations Give Rise to Internal Friction in Unfolded Proteins
inferredcites →https://doi.org/10.1021/ja802124eopenalex-snapshot
Natively Unfolded Protein Stability as a Coil-to-Globule Transition in Charge/Hydropathy Space
inferredcites →https://doi.org/10.1021/ja808305uopenalex-snapshot
Protein Folding, Protein Collapse, and Tanford’s Transfer Model: Lessons from Single-Molecule FRET
inferredcites →https://doi.org/10.1021/jacs.6b05443openalex-snapshot
Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment
inferredcites →https://doi.org/10.1021/jacs.6b05917openalex-snapshot
Consistent View of Polypeptide Chain Expansion in Chemical Denaturants from Multiple Experimental Methods
inferredcites →https://doi.org/10.1021/jacs.6b10272openalex-snapshot
Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation
inferredcites →https://doi.org/10.1021/jp076971jopenalex-snapshot
Unfolded Protein and Peptide Dynamics Investigated with Single-Molecule FRET and Correlation Spectroscopy from Picoseconds to Seconds
inferredcites →https://doi.org/10.1021/jp508971mopenalex-snapshot
Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
inferredcites →https://doi.org/10.1021/la4013922openalex-snapshot
Morphology of Polymer Brushes Infiltrated by Attractive Nanoinclusions of Various Sizes
inferredcites →https://doi.org/10.1021/ma60071a040openalex-snapshot
Phase Transition Behavior of the Isolated Polymer Chain
inferredcites →https://doi.org/10.1038/cr.2009.87openalex-snapshot
Predicting intrinsic disorder in proteins: an overview
inferredcites →https://doi.org/10.1038/nchem.2715openalex-snapshot
Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity
inferredcites →https://doi.org/10.1038/ncomms5307openalex-snapshot
Molecular origins of internal friction effects on protein-folding rates
inferredcites →https://doi.org/10.1038/nphys3532openalex-snapshot
Polymer physics of intracellular phase transitions
inferredcites →https://doi.org/10.1039/b717350dopenalex-snapshot
Brownian dynamics simulation of polymer collapse in a poor solvent: influence of implicit hydrodynamic interactions
inferredcites →https://doi.org/10.1042/bj20121346openalex-snapshot
Describing sequence–ensemble relationships for intrinsically disordered proteins
inferredcites →https://doi.org/10.1051/jphyslet:019850046015068900openalex-snapshot
Long polymers in good solvent : ε-expansion of the ratio of the radius of gyration to the end to end distance
inferredcites →https://doi.org/10.1051/sfn/201112010openalex-snapshot
nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions
inferredcites →https://doi.org/10.1063/1.1483296openalex-snapshot
Corrections to scaling in the hydrodynamic properties of dilute polymer solutions
inferredcites →https://doi.org/10.1063/1.1532728openalex-snapshot
Non-Gaussian dynamics from a simulation of a short peptide: Loop closure rates and effective diffusion coefficients
inferredcites →https://doi.org/10.1063/1.1564047openalex-snapshot
Translational diffusion of polymer chains with excluded volume and hydrodynamic interactions by Brownian dynamics simulation
inferredcites →https://doi.org/10.1063/1.1673799openalex-snapshot
Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction
inferredcites →https://doi.org/10.1063/1.1740494openalex-snapshot
Errata: The Intrinsic Viscosities and Diffusion Constants of Flexible Macromolecules in Solution
inferredcites →https://doi.org/10.1063/1.1746947openalex-snapshot
The Intrinsic Viscosities and Diffusion Constants of Flexible Macromolecules in Solution
inferredcites →https://doi.org/10.1063/1.1846651openalex-snapshot
A molecular dynamics study on universal properties of polymer chains in different solvent qualities. Part I. A review of linear chain properties
inferredcites →https://doi.org/10.1063/1.3626868openalex-snapshot
Comparison of Brownian dynamics algorithms with hydrodynamic interaction
inferredcites →https://doi.org/10.1063/1.436761openalex-snapshot
Brownian dynamics with hydrodynamic interactions
inferredcites →https://doi.org/10.1063/1.4792206openalex-snapshot
Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models
inferredcites →https://doi.org/10.1063/1.4929391openalex-snapshot
A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
inferredcites →https://doi.org/10.1063/1.5009286openalex-snapshot
Internal friction in an intrinsically disordered protein—Comparing Rouse-like models with experiments
inferredcites →https://doi.org/10.1063/1.5037683openalex-snapshot
Perspective: Chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET
inferredcites →https://doi.org/10.1063/1.533249openalex-snapshot
Probability distribution of distance in a uniform ellipsoid: Theory and applications to physics
inferredcites →https://doi.org/10.1063/1.881812openalex-snapshot
Understanding Molecular Simulation: From Algorithms to Applications
inferredcites →https://doi.org/10.1073/pnas.0611093104openalex-snapshot
Ultrafast dynamics of protein collapse from single-molecule photon statistics
inferredcites →https://doi.org/10.1073/pnas.1001743107openalex-snapshot
Charge interactions can dominate the dimensions of intrinsically disordered proteins
inferredcites →https://doi.org/10.1073/pnas.1117368109openalex-snapshot
Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy
inferredcites →https://doi.org/10.1073/pnas.1207719109openalex-snapshot
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
inferredcites →https://doi.org/10.1073/pnas.1212909110openalex-snapshot
Effect of charge, hydrophobicity, and sequence of nucleoporins on the translocation of model particles through the nuclear pore complex
inferredcites →https://doi.org/10.1073/pnas.1300596110openalex-snapshot
Elasticity, structure, and relaxation of extended proteins under force
inferredcites →https://doi.org/10.1073/pnas.1304749110openalex-snapshot
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
inferredcites →https://doi.org/10.1073/pnas.1418673112openalex-snapshot
Random coil negative control reproduces the discrepancy between scattering and FRET measurements of denatured protein dimensions
inferredcites →https://doi.org/10.1073/pnas.1704692114openalex-snapshot
Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
inferredcites →https://doi.org/10.1073/pnas.1813038116openalex-snapshot
Commonly used FRET fluorophores promote collapse of an otherwise disordered protein
inferredcites →https://doi.org/10.1074/mcp.m000035-mcp201openalex-snapshot
A Bimodal Distribution of Two Distinct Categories of Intrinsically Disordered Structures with Separate Functions in FG Nucleoporins
inferredcites →https://doi.org/10.1080/21690707.2015.1135015openalex-snapshot
Paradoxes and wonders of intrinsic disorder: Complexity of simplicity
inferredcites →https://doi.org/10.1088/0305-4470/35/7/302openalex-snapshot
Universal amplitude ratios for three-dimensional self-avoiding walks
inferredcites →https://doi.org/10.1088/0953-8984/23/3/033102openalex-snapshot
Hydrodynamic effects in proteins
inferredcites →https://doi.org/10.1093/oso/9780198517726.001.0001openalex-snapshot
Introduction to Polymer Physics
inferredcites →https://doi.org/10.1103/physreve.101.022420openalex-snapshot
Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics
inferredcites →https://doi.org/10.1103/physreve.86.031806openalex-snapshot
Morphological control of grafted polymer films via attraction to small nanoparticle inclusions
inferredcites →https://doi.org/10.1103/physrevlett.80.4092openalex-snapshot
Globule-to-Coil Transition of a Single Homopolymer Chain in Solution
inferredcites →https://doi.org/10.1139/o09-169openalex-snapshot
Molecular simulations of protein disorderThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer…
inferredcites →https://doi.org/10.1140/epje/i2012-12130-xopenalex-snapshot
Translational diffusion coefficients of macromolecules
inferredcites →https://doi.org/10.1146/annurev-biochem-072711-164947openalex-snapshot
Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions
inferredcites →https://doi.org/10.1146/annurev-biophys-070317-032838openalex-snapshot
Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions
inferredcites →https://doi.org/10.1146/annurev-physchem-052516-050843openalex-snapshot
Computer Simulations of Intrinsically Disordered Proteins
inferredcites →https://doi.org/10.1186/1471-2164-9-s2-s1openalex-snapshot
The unfoldomics decade: an update on intrinsically disordered proteins
inferredcites →https://doi.org/10.3390/polym6102684openalex-snapshot
Intrinsically Disordered Proteins: Where Computation Meets Experiment
inferredcites →https://doi.org/10.4161/idp.24360openalex-snapshot
The alphabet of intrinsic disorder
inferredcites →https://doi.org/10.5860/choice.33-2140openalex-snapshot
Principles of polymer chemistry
inferredcites →https://doi.org/10.7554/elife.10785openalex-snapshot
Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex
inferredcites →https://doi.org/10.7554/elife.14119openalex-snapshot
A physical model describing the interaction of nuclear transport receptors with FG nucleoporin domain assemblies

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.bpj.2021.01.039openalex-snapshot
Physical modeling of multivalent interactions in the nuclear pore complex
inferred← citeshttps://doi.org/10.1016/j.cocis.2021.101457openalex-snapshot
Polyampholyte physics: Liquid–liquid phase separation and biological condensates
inferred← citeshttps://doi.org/10.1021/acs.biomac.2c00866openalex-snapshot
Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles
inferred← citeshttps://doi.org/10.1073/pnas.2212874120openalex-snapshot
Self-regulation of the nuclear pore complex enables clogging-free crowded transport
inferred← citeshttps://doi.org/10.1101/2022.10.28.514176openalex-snapshot
Self-Assembly of Tunable Intrinsically Disordered Peptide Amphiphiles
Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.