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References from Studies on Molecular Dynamics of Intrinsically Disordered Proteins and Their Fuzzy Complexes: A Mini-Review. Local targets link to admitted publications; unresolved targets remain external evidence.
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So much more to know …
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Molecular dynamics simulations of a reversibly folding β-Heptapeptide in methanol: influence of the treatment of long-range electrostatic interactions
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Enhanced sampling of molecular dynamics simulations of a Polyalanine Octapeptide: effects of the periodic boundary conditions on peptide conformation
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Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system
10.1063/1.4827055 · 2013 · External reference
The zero-multipole summation method for estimating electrostatic interactions in molecular dynamics: analysis of the accuracy and application to liquid systems
10.1063/1.4875693 · 2014 · External reference
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Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent
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Ensuring mixing efficiency of replica-exchange molecular dynamics simulations
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Exchange frequency in replica exchange molecular dynamics
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Error and efficiency of replica exchange molecular dynamics simulations
10.1063/1.3249608 · 2009 · External reference
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Structural and kinetic characterization of the intrinsically disordered protein SeV NTAIL through enhanced sampling simulations
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Conformational ensembles of an intrinsically disordered protein pKID with and without a KIX domain in explicit solvent investigated by all-atom multicanonical molecular dynamics
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Simulation of coupled folding and binding of an intrinsically disordered protein in explicit solvent with metadynamics
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Modeling the relationship between the p53 C-terminal domain and its binding partners using molecular dynamics
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Long range recognition and selection in IDPs: the interactions of the C-terminus of p53
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The transient manifold structure of the p53 extreme C-terminal domain: insight into disorder, recognition, and binding promiscuity by molecular dynamics simulations
10.1039/c7cp02485a · 2017 · External reference
Intrinsically disordered p53 extreme C-terminus binds to S100B(ββ) through “fly-casting”
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Binding of two intrinsically disordered peptides to a multi-specific protein: a combined Monte Carlo and Molecular dynamics study
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Multimodal structural distribution of the p53 C-terminal domain upon binding to S100B via a generalized ensemble method: from disorder to extradisorder
10.1021/acs.jctc.8b01042 · 2019 · External reference
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Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state
2018 · External reference
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Unresolved reference
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Oligomer formation of amyloid-β(29–42) from its monomers using the Hamiltonian replica-permutation molecular dynamics simulation
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The dynamic multisite interactions between two intrinsically disordered proteins
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myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme
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Temperature-controlled liquid–liquid phase separation of disordered proteins
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CAMELOT: a machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences
10.1063/1.4935066 · 2015 · External reference
A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins
10.1016/j.cell.2018.06.006 · 2018 · External reference
Binding mechanisms of intrinsically disordered proteins: theory, simulation, and experiment
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Density functional study of molecular interactions in secondary structures of proteins
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Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach
2019 · External reference
