On the public citation graph

Comparison of force fields for Alzheimer's A: A case study for intrinsically disordered proteins

0 signed · 228 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 See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.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/(sici)1096-987x(199906)20:8<786::aid-jcc5>3.0.co;2-bopenalex-snapshot

Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems

inferredcites →https://doi.org/10.1002/(sici)1521-3773(19990115)38:1/2<236::aid-anie236>3.0.co;2-mopenalex-snapshot

Peptide Folding: When Simulation Meets Experiment

inferredcites →https://doi.org/10.1002/ange.201001898openalex-snapshot

NMR‐Based Protein Potentials

inferredcites →https://doi.org/10.1002/anie.201001898openalex-snapshot

NMR‐Based Protein Potentials

inferredcites →https://doi.org/10.1002/bip.360221211openalex-snapshot

Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features

inferredcites →https://doi.org/10.1002/cphc.201500415openalex-snapshot

The Dependence of Amyloid‐β Dynamics on Protein Force Fields and Water Models

inferredcites →https://doi.org/10.1002/jcc.20082openalex-snapshot

Empirical force fields for biological macromolecules: Overview and issues

inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot

Scalable molecular dynamics with NAMD

inferredcites →https://doi.org/10.1002/jcc.21209openalex-snapshot

Accelerating molecular dynamic simulation on graphics processing units

inferredcites →https://doi.org/10.1002/jcc.21787openalex-snapshot

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

inferredcites →https://doi.org/10.1002/jcc.23973openalex-snapshot

Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation

inferredcites →https://doi.org/10.1002/jcc.23996openalex-snapshot

Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis

inferredcites →https://doi.org/10.1002/jcc.540130805openalex-snapshot

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models

inferredcites →https://doi.org/10.1002/prot.21123openalex-snapshot

Comparison of multiple Amber force fields and development of improved protein backbone parameters

inferredcites →https://doi.org/10.1002/prot.22711openalex-snapshot

Improved side‐chain torsion potentials for the Amber ff99SB protein force field

inferredcites →https://doi.org/10.1007/978-94-007-7606-7openalex-snapshot

An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation

inferredcites →https://doi.org/10.1007/bf00211764openalex-snapshot

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

inferredcites →https://doi.org/10.1007/bf00227471openalex-snapshot

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects

inferredcites →https://doi.org/10.1007/bfb0105461openalex-snapshot

Error estimates on averages of correlated data

inferredcites →https://doi.org/10.1007/s10858-010-9433-9openalex-snapshot

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot

VMD: Visual molecular dynamics

inferredcites →https://doi.org/10.1016/j.bpj.2011.03.051openalex-snapshot

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

inferredcites →https://doi.org/10.1016/j.bpj.2011.12.002openalex-snapshot

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

inferredcites →https://doi.org/10.1016/j.bpj.2012.09.032openalex-snapshot

The Conformational Ensembles of α-Synuclein and Tau: Combining Single-Molecule FRET and Simulations

inferredcites →https://doi.org/10.1016/j.bpj.2012.11.009openalex-snapshot

Effects of Familial Mutations on the Monomer Structure of Aβ42

inferredcites →https://doi.org/10.1016/j.bpj.2013.04.056openalex-snapshot

Differences in β-strand Populations of Monomeric Aβ40 and Aβ42

inferredcites →https://doi.org/10.1016/j.bpj.2014.12.013openalex-snapshot

Alzheimer’s Protective A2T Mutation Changes the Conformational Landscape of the Aβ1–42 Monomer Differently Than Does the A2V Mutation

inferredcites →https://doi.org/10.1016/j.bpj.2016.04.027openalex-snapshot

Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F

inferredcites →https://doi.org/10.1016/j.jmb.2004.02.002openalex-snapshot

Prediction and Functional Analysis of Native Disorder in Proteins from the Three Kingdoms of Life

inferredcites →https://doi.org/10.1016/j.jmb.2006.09.046openalex-snapshot

Aβ42 is More Rigid than Aβ40 at the C Terminus: Implications for Aβ Aggregation and Toxicity

inferredcites →https://doi.org/10.1016/j.jmb.2007.02.093openalex-snapshot

The Alzheimer’s Peptides Aβ40 and 42 Adopt Distinct Conformations in Water: A Combined MD / NMR Study

inferredcites →https://doi.org/10.1016/j.jmb.2009.01.029openalex-snapshot

The Structure of Aβ42 C-Terminal Fragments Probed by a Combined Experimental and Theoretical Study

inferredcites →https://doi.org/10.1016/j.jmb.2010.10.015openalex-snapshot

Atomic-Level Characterization of the Ensemble of the Aβ(1–42) Monomer in Water Using Unbiased Molecular Dynamics Simulations and Spectral Algorithms

inferredcites →https://doi.org/10.1016/j.jmb.2013.06.021openalex-snapshot

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

inferredcites →https://doi.org/10.1016/j.pbiomolbio.2015.03.003openalex-snapshot

Progress in studying intrinsically disordered proteins with atomistic simulations

inferredcites →https://doi.org/10.1016/j.sbi.2011.03.011openalex-snapshot

Intrinsically disordered proteins: regulation and disease

inferredcites →https://doi.org/10.1016/j.sbi.2013.12.006openalex-snapshot

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

inferredcites →https://doi.org/10.1016/s0009-2614(97)01198-6openalex-snapshot

Parallel tempering algorithm for conformational studies of biological molecules

inferredcites →https://doi.org/10.1016/s0009-2614(99)01123-9openalex-snapshot

Replica-exchange molecular dynamics method for protein folding

inferredcites →https://doi.org/10.1021/acs.biochem.5b01259openalex-snapshot

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

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.jpcb.5b04822openalex-snapshot

Oligomer Formation of Toxic and Functional Amyloid Peptides Studied with Atomistic Simulations

inferredcites →https://doi.org/10.1021/acs.jpcb.5b09379openalex-snapshot

Characterization of Aβ Monomers through the Convergence of Ensemble Properties among Simulations with Multiple Force Fields

inferredcites →https://doi.org/10.1021/acs.jpclett.6b00518openalex-snapshot

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

inferredcites →https://doi.org/10.1021/bi200732xopenalex-snapshot

Homogeneous and Heterogeneous Tertiary Structure Ensembles of Amyloid-β Peptides

inferredcites →https://doi.org/10.1021/cr500638nopenalex-snapshot

Amyloid β Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies

inferredcites →https://doi.org/10.1021/ct2007814openalex-snapshot

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

inferredcites →https://doi.org/10.1021/ct300323gopenalex-snapshot

Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations

inferredcites →https://doi.org/10.1021/ct300400xopenalex-snapshot

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles

inferredcites →https://doi.org/10.1021/ct500569bopenalex-snapshot

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association

inferredcites →https://doi.org/10.1021/ct500718sopenalex-snapshot

Accuracy of Current All-Atom Force-Fields in Modeling Protein Disordered States

inferredcites →https://doi.org/10.1021/ct501178zopenalex-snapshot

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: Force Field Evaluation and Comparison with Experiment

inferredcites →https://doi.org/10.1021/ct700200bopenalex-snapshot

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation

inferredcites →https://doi.org/10.1021/ct700301qopenalex-snapshot

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

inferredcites →https://doi.org/10.1021/ct9000685openalex-snapshot

ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

inferredcites →https://doi.org/10.1021/ja0000908openalex-snapshot

Prediction of Sterically Induced Alignment in a Dilute Liquid Crystalline Phase: Aid to Protein Structure Determination by NMR

inferredcites →https://doi.org/10.1021/ja00070a024openalex-snapshot

Quantitative J correlation: a new approach for measuring homonuclear three-bond J(HNH.alpha.) coupling constants in 15N-enriched proteins

inferredcites →https://doi.org/10.1021/ja036813fopenalex-snapshot

Solution NMR Studies of the Aβ(1−40) and Aβ(1−42) Peptides Establish that the Met35 Oxidation State Affects the Mechanism of Amyloid Formation

inferredcites →https://doi.org/10.1021/ja403147mopenalex-snapshot

Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation

inferredcites →https://doi.org/10.1021/ja710366copenalex-snapshot

Structure and Dynamics of the Aβ21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations

inferredcites →https://doi.org/10.1021/ja711189copenalex-snapshot

M35 Oxidation Induces Aβ40-like Structural and Dynamical Changes in Aβ42

inferredcites →https://doi.org/10.1021/jp2076337openalex-snapshot

Structures of the Amyloid β-Peptides Aβ1–40 and Aβ1–42 as Influenced by pH and a d -Peptide

inferredcites →https://doi.org/10.1021/jp4115404openalex-snapshot

Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer

inferredcites →https://doi.org/10.1021/jp5034245openalex-snapshot

Hot Spot of Structural Ambivalence in Prion Protein Revealed by Secondary Structure Principal Component Analysis

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/jp900425eopenalex-snapshot

Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

inferredcites →https://doi.org/10.1021/jp901540topenalex-snapshot

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

inferredcites →https://doi.org/10.1038/ncomms6773openalex-snapshot

A fully atomistic computer simulation study of cold denaturation of a β-hairpin

inferredcites →https://doi.org/10.1038/nprot.2008.36openalex-snapshot

NMR: prediction of molecular alignment from structure using the PALES software

inferredcites →https://doi.org/10.1038/srep11024openalex-snapshot

Varied Probability of Staying Collapsed/Extended at the Conformational Equilibrium of Monomeric Aβ40 and Aβ42

inferredcites →https://doi.org/10.1046/j.1432-1033.2002.03271.xopenalex-snapshot

Solution structure of the Alzheimer amyloid β‐peptide (1–42) in an apolar microenvironment

inferredcites →https://doi.org/10.1063/1.1683075openalex-snapshot

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

inferredcites →https://doi.org/10.1063/1.1729860openalex-snapshot

Contact Electron-Spin Coupling of Nuclear Magnetic Moments

inferredcites →https://doi.org/10.1063/1.328693openalex-snapshot

Polymorphic transitions in single crystals: A new molecular dynamics method

inferredcites →https://doi.org/10.1063/1.3565032openalex-snapshot

Markov models of molecular kinetics: Generation and validation

inferredcites →https://doi.org/10.1063/1.3660669openalex-snapshot

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

inferredcites →https://doi.org/10.1063/1.447334openalex-snapshot

A unified formulation of the constant temperature molecular dynamics methods

inferredcites →https://doi.org/10.1063/1.457480openalex-snapshot

Error estimates on averages of correlated data

inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems

inferredcites →https://doi.org/10.1063/1.4904890openalex-snapshot

On performance measures for infinite swapping Monte Carlo methods

inferredcites →https://doi.org/10.1063/1.4909549openalex-snapshot

Dynamic properties of force fields

inferredcites →https://doi.org/10.1073/pnas.0408153101openalex-snapshot

In silico study of amyloid β-protein folding and oligomerization

inferredcites →https://doi.org/10.1074/jbc.m110.199885openalex-snapshot

Nature of the Amyloid-β Monomer and the Monomer-Oligomer Equilibrium

inferredcites →https://doi.org/10.1074/jbc.m201750200openalex-snapshot

Oligomeric and Fibrillar Species of Amyloid-β Peptides Differentially Affect Neuronal Viability

inferredcites →https://doi.org/10.1080/00268978300102851openalex-snapshot

Constant pressure molecular dynamics for molecular systems

inferredcites →https://doi.org/10.1080/07391102.2013.838518openalex-snapshot

Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide

inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot

Canonical dynamics: Equilibrium phase-space distributions

inferredcites →https://doi.org/10.1103/physrevb.33.339openalex-snapshot

Constant-temperature–constant-pressure molecular-dynamics calculations for molecular solids: Application to solid nitrogen at high pressure

inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot

Matplotlib: A 2D Graphics Environment

inferredcites →https://doi.org/10.1145/1250662openalex-snapshot

Proceedings of the 34th annual international symposium on Computer architecture

inferredcites →https://doi.org/10.1146/annurev.biochem.75.101304.123901openalex-snapshot

Protein Misfolding, Functional Amyloid, and Human Disease

inferredcites →https://doi.org/10.1371/journal.pone.0032131openalex-snapshot

Systematic Validation of Protein Force Fields against Experimental Data

inferredcites →https://doi.org/10.1371/journal.pone.0134091openalex-snapshot

Secondary Structure of Rat and Human Amylin across Force Fields

inferredcites →https://doi.org/10.1529/biophysj.108.132696openalex-snapshot

Are Current Molecular Dynamics Force Fields too Helical?

inferredcites →https://doi.org/10.3390/e16010163openalex-snapshot

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

What points at this work

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

inferred← citeshttps://doi.org/10.2139/ssrn.4794987openalex-extracted

Virtual Screening Strategies in Drug Discovery: Potential Inhibitors of Candida Albicans Cytochrome B

inferred← citeshttps://doi.org/10.2139/ssrn.4820229openalex-extracted

Virtual Screening Strategies in Drug Discovery: Potential Inhibitors of Candida Albicans Cytochrome B

inferred← citeshttps://doi.org/10.1002/cphc.202400502openalex-snapshot

Dimerization of Full‐Length Aβ‐42 Peptide: A Comparison of Different Force Fields and Water Models

inferred← citeshttps://doi.org/10.1002/prot.25525openalex-snapshot

How accurately do force fields represent protein side chain ensembles?

inferred← citeshttps://doi.org/10.1002/prot.26590openalex-snapshot

Atomistic molecular simulations of Aβ‐Zn conformational ensembles

inferred← citeshttps://doi.org/10.1002/wcms.1359openalex-snapshot

Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment

inferred← citeshttps://doi.org/10.1002/wcms.1703openalex-snapshot

A brief history of amyloid aggregation simulations

inferred← citeshttps://doi.org/10.1007/978-1-0716-1546-1_18openalex-snapshot

Characterization of Amyloidogenic Peptide Aggregability in Helical Subspace

inferred← citeshttps://doi.org/10.1007/978-1-4939-9678-0_17openalex-snapshot

Atomistic Simulation Tools to Study Protein Self-Aggregation

inferred← citeshttps://doi.org/10.1007/978-981-15-8936-2_13openalex-snapshot

Molecular Dynamic Simulation of Intrinsically Disordered Proteins and Relevant Forcefields

inferred← citeshttps://doi.org/10.1007/s00018-018-2798-8openalex-snapshot

Biochemical, biophysical and molecular dynamics studies on the proteoglycan-like domain of carbonic anhydrase IX

inferred← citeshttps://doi.org/10.1007/s00249-019-01407-xopenalex-snapshot

Effect of lipid saturation on amyloid-beta peptide partitioning and aggregation in neuronal membranes: molecular dynamics simulations

inferred← citeshttps://doi.org/10.1007/s00894-019-4137-xopenalex-snapshot

Synergistic long-range effects of mutations underlie aggregation propensities of amylin analogues

inferred← citeshttps://doi.org/10.1007/s00894-020-04379-4openalex-snapshot

Structural analyses and force fields comparison for NACore (68–78) and SubNACore (69–77) fibril segments of Parkinson’s disease

inferred← citeshttps://doi.org/10.1007/s11433-017-9124-3openalex-snapshot

Atomistic simulation of the coupled adsorption and unfolding of protein GB1 on the polystyrenes nanoparticle surface

inferred← citeshttps://doi.org/10.1007/s12551-021-00850-5openalex-snapshot

Secondary structure dependence on simulation techniques and force field parameters: from disordered to ordered proteins

inferred← citeshttps://doi.org/10.1007/s12551-024-01253-yopenalex-snapshot

Survey of the Aβ-peptide structural diversity: molecular dynamics approaches

inferred← citeshttps://doi.org/10.1016/bs.apcsb.2019.10.001openalex-snapshot

Combining molecular dynamics simulations and experimental analyses in protein misfolding

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2019.05.007openalex-snapshot

Intrinsically disordered proteins in various hypotheses on the pathogenesis of Alzheimer's and Parkinson's diseases

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2019.12.002openalex-snapshot

Aggregation of disease-related peptides

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2019.12.009openalex-snapshot

Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2020.01.002openalex-snapshot

Long-time methods for molecular dynamics simulations: Markov State Models and Milestoning

inferred← citeshttps://doi.org/10.1016/bs.pmbts.2021.06.003openalex-snapshot

Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions

inferred← citeshttps://doi.org/10.1016/j.bbamem.2018.03.026openalex-snapshot

Physiologically-relevant levels of sphingomyelin, but not GM1, induces a β-sheet-rich structure in the amyloid-β(1-42) monomer

inferred← citeshttps://doi.org/10.1016/j.bbrc.2024.150720openalex-snapshot

Comparative study of stability and activity of wild-type and mutant human carbonic anhydrase II enzymes using molecular dynamics and docking simulations

inferred← citeshttps://doi.org/10.1016/j.bpc.2020.106531openalex-snapshot

A lowly populated, transient β-sheet structure in monomeric Aβ1-42 identified by multinuclear NMR of chemical denaturation

inferred← citeshttps://doi.org/10.1016/j.bpc.2021.106631openalex-snapshot

Comparison of the force fields on monomeric and fibrillar PHF6 of tau protein

inferred← citeshttps://doi.org/10.1016/j.bpj.2018.04.028openalex-snapshot

Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein

inferred← citeshttps://doi.org/10.1016/j.bpj.2018.11.3143openalex-snapshot

Structural Analysis of a Trimer of β2-Microgloblin Fragment by Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1016/j.chemphys.2020.111057openalex-snapshot

Investigation of the stability and the helix-tail interaction of sCT and its various charged mutants based on comparative molecular dynamics simulations

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2020.09.230openalex-snapshot

DSS1 allosterically regulates the conformation of the tower domain of BRCA2 that has dsDNA binding specificity for homologous recombination

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2021.06.078openalex-snapshot

Molecular insight into the early stage of amyloid-β(1-42) Homodimers aggregation influenced by histidine tautomerism

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2022.06.007openalex-snapshot

Histidine tautomerism dependent conformational transitions driven aggregation of profilin-1: Implications in amyotrophic lateral sclerosis

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.123403openalex-snapshot

Mechanistic insights into the conformational switch in profilin-1 subject to collective effects of mutation and histidine tautomerism

inferred← citeshttps://doi.org/10.1016/j.jics.2023.100892openalex-snapshot

Theoretical investigations of TTR derived aggregation-prone peptides’ potential to biochemically attenuate the amyloidogenic propensities of V30 M TTR amyloid fibrils

inferred← citeshttps://doi.org/10.1016/j.jmgm.2019.01.009openalex-snapshot

Efficient construction of a diverse conformational library for amyloid-β as an intrinsically disordered protein

inferred← citeshttps://doi.org/10.1016/j.jsb.2020.107573openalex-snapshot

Structural ensemble and biological activity of DciA intrinsically disordered region

inferred← citeshttps://doi.org/10.1016/j.sbi.2017.10.008openalex-snapshot

Force field development and simulations of intrinsically disordered proteins

inferred← citeshttps://doi.org/10.1021/acs.biochem.5c00139openalex-snapshot

Polyphenolic Gallotannins 1,3,6-Tri-O-galloyl-β- d -glucose and Corilagin Attenuate IAPP Amyloid Formation and Cytotoxicity by Primarily Targeting Secondary Nucleation

inferred← citeshttps://doi.org/10.1021/acs.biochem.7b00344openalex-snapshot

Identification of Key Interactions in the Initial Self-Assembly of Amylin in a Membrane Environment

inferred← citeshttps://doi.org/10.1021/acs.chemrev.0c01122openalex-snapshot

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00059openalex-snapshot

Environment-Specific Force Field for Intrinsically Disordered and Ordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01063openalex-snapshot

Different Force Fields Give Rise to Different Amyloid Aggregation Pathways in Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01202openalex-snapshot

Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning

inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01624openalex-snapshot

Structure Comparison of Beta Amyloid Peptide Aβ 1–42 Isoforms. Molecular Dynamics Modeling

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00809openalex-snapshot

Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering

inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00965openalex-snapshot

Wild-Type α-Synuclein Structure and Aggregation: A Comprehensive Coarse-Grained and All-Atom Molecular Dynamics Study

inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00761openalex-snapshot

Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins

inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01001openalex-snapshot

N-Terminal Chirality and Sequence Variations Modulate the Conformational Landscape of Amyloid-Beta 42

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00926openalex-snapshot

Alanine Scanning Effects on the Biochemical and Biophysical Properties of Intrinsically Disordered Proteins: A Case Study of the Histidine to Alanine Mutations in Amyloid-β 42

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00928openalex-snapshot

Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles

inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00983openalex-snapshot

Transition Metal Ion Interactions with Disordered Amyloid-β Peptides in the Pathogenesis of Alzheimer’s Disease: Insights from Computational Chemistry Studies

inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00080openalex-snapshot

Exploiting a Mechanical Perturbation of a Titin Domain to Identify How Force Field Parameterization Affects Protein Refolding Pathways

inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00948openalex-snapshot

Assessing SIRAH’s Capability to Simulate Intrinsically Disordered Proteins and Peptides

inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00889openalex-snapshot

Modeling the Structure and Interactions of Intrinsically Disordered Peptides with Multiple Replica, Metadynamics-Based Sampling Methods and Force-Field Combinations

inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00971openalex-snapshot

Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation

inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00183openalex-snapshot

Intrinsic Conformational Preferences and Interactions in α-Synuclein Fibrils: Insights from Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jctc.8b00579openalex-snapshot

On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jctc.8b01107openalex-snapshot

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ 16–22 Dimer

inferred← citeshttps://doi.org/10.1021/acs.jctc.9b00338openalex-snapshot

SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c00771openalex-snapshot

Computational Model to Unravel the Function of Amyloid-β Peptides in Contact with a Phospholipid Membrane

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c01360openalex-snapshot

Occurrence of Biased Conformations as Precursors of Assembly States in Fibril Elongation of Amyloid-β Fibril Variants: An In Silico Study

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c05508openalex-snapshot

Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c06000openalex-snapshot

Molecular Insight into the Effects of Enhanced Hydrophobicity on Amyloid-like Aggregation

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c08702openalex-snapshot

Conformational Preferences of an Intrinsically Disordered Protein Domain: A Case Study for Modern Force Fields

inferred← citeshttps://doi.org/10.1021/acs.jpcb.0c09617openalex-snapshot

Effects of Ions and Small Compounds on the Structure of Aβ42 Monomers

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c04743openalex-snapshot

Characterization of the Conformations of Amyloid Beta 42 in Solution That May Mediate Its Initial Hydrophobic Aggregation

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c07321openalex-snapshot

Insights into the Mixture of Aβ24 and Aβ42 Peptides from Atomistic Simulations

inferred← citeshttps://doi.org/10.1021/acs.jpcb.3c07861openalex-snapshot

Peptide Self-Assembly into Amyloid Fibrils: Unbiased All-Atom Simulations

inferred← citeshttps://doi.org/10.1021/acs.jpcb.4c00503openalex-snapshot

Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b00267openalex-snapshot

Conformational Ensembles of the Wild-Type and S8C Aβ1–42 Dimers

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b04689openalex-snapshot

High-Resolution Structures of the Amyloid-β 1–42 Dimers from the Comparison of Four Atomistic Force Fields

inferred← citeshttps://doi.org/10.1021/acs.jpcb.7b12528openalex-snapshot

Structural Interconversion in Alzheimer’s Amyloid-β(16–35) Peptide in an Aqueous Solution

inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b02727openalex-snapshot

Inhibitory Effect of Choline-O-sulfate on Aβ16–22 Peptide Aggregation: A Molecular Dynamics Simulation Study

inferred← citeshttps://doi.org/10.1021/acs.jpcb.9b04208openalex-snapshot

Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acs.jpclett.8b02375openalex-snapshot

Molecular Determinants of Aβ 42 Adsorption to Amyloid Fibril Surfaces

inferred← citeshttps://doi.org/10.1021/acscentsci.7b00626openalex-snapshot

Looking at the Disordered Proteins through the Computational Microscope

inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00163openalex-snapshot

Structural Characteristics of Monomeric Aβ42 on Fibril in the Early Stage of Secondary Nucleation Process

inferred← citeshttps://doi.org/10.1021/acschemneuro.7b00396openalex-snapshot

Islet Amyloid Polypeptide Promotes Amyloid-Beta Aggregation by Binding-Induced Helix-Unfolding of the Amyloidogenic Core

inferred← citeshttps://doi.org/10.1021/acschemneuro.8b00091openalex-snapshot

Compound CID 9998128 Is a Potential Multitarget Drug for Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1021/acschemneuro.9b00558openalex-snapshot

Role of Oxidized Gly25, Gly29, and Gly33 Residues on the Interactions of Aβ1–42 with Lipid Membranes

inferred← citeshttps://doi.org/10.1021/acsomega.0c02051openalex-snapshot

Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor

inferred← citeshttps://doi.org/10.1021/acsomega.0c02983openalex-snapshot

Impact of Mutations on the Conformational Transition from α-Helix to β-Sheet Structures in Arctic-Type Aβ40: Insights from Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.1021/acsomega.5c01677openalex-snapshot

Conformational Flexibility of GRB2 as a Key Factor in the Stability and Regulation of Its Interaction with SOS1

inferred← citeshttps://doi.org/10.1021/acsomega.7b00018openalex-snapshot

Influence of Hyperglycemic Conditions on Self-Association of the Alzheimer’s Amyloid β (Aβ1–42) Peptide

inferred← citeshttps://doi.org/10.1021/jacs.9b04995openalex-snapshot

The Mitochondrial Peptide Humanin Targets but Does Not Denature Amyloid Oligomers in Type II Diabetes

inferred← citeshttps://doi.org/10.1038/s41598-017-10212-5openalex-snapshot

Emergence of Alternative Structures in Amyloid Beta 1-42 Monomeric Landscape by N-terminal Hexapeptide Amyloid Inhibitors

inferred← citeshttps://doi.org/10.1038/s41598-020-64303-xopenalex-snapshot

Long-range Regulation of Partially Folded Amyloidogenic Peptides

inferred← citeshttps://doi.org/10.1039/c9cp00859dopenalex-snapshot

The interactions of an Aβ protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances

inferred← citeshttps://doi.org/10.1039/c9cp02765copenalex-snapshot

Computational insights into lipid assisted peptide misfolding and aggregation in neurodegeneration

inferred← citeshttps://doi.org/10.1039/c9cp04162aopenalex-snapshot

Caffeine destabilizes preformed Aβ protofilaments: insights from all atom molecular dynamics simulations

inferred← citeshttps://doi.org/10.1039/c9ra04637bopenalex-snapshot

Replica exchange molecular dynamics simulation of the coordination of Pt( ii )-Phenanthroline to amyloid-β

inferred← citeshttps://doi.org/10.1039/c9ra06424aopenalex-snapshot

Modelling of interactions between Aβ(25–35) peptide and phospholipid bilayers: effects of cholesterol and lipid saturation

inferred← citeshttps://doi.org/10.1039/d0cc06607aopenalex-snapshot

Compact fibril-like structure of amyloid β-peptide (1–42) monomers

inferred← citeshttps://doi.org/10.1039/d0na00941eopenalex-snapshot

Folding and self-assembly of short intrinsically disordered peptides and protein regions

inferred← citeshttps://doi.org/10.1039/d0sc04657dopenalex-snapshot

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

inferred← citeshttps://doi.org/10.1039/d1cp00825kopenalex-snapshot

Controlling the self-assembly of human calcitonin: a theoretical approach using molecular dynamics simulations

inferred← citeshttps://doi.org/10.1063/1.4979516openalex-snapshot

Cooperative structural transitions in amyloid-like aggregation

inferred← citeshttps://doi.org/10.1063/1.4979866openalex-snapshot

Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42)

inferred← citeshttps://doi.org/10.1063/1.5004774openalex-snapshot

Peptide dimerization-dissociation rates from replica exchange molecular dynamics

inferred← citeshttps://doi.org/10.1063/1.5027580openalex-snapshot

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides

inferred← citeshttps://doi.org/10.1063/1.5083915openalex-snapshot

Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly

inferred← citeshttps://doi.org/10.1063/1.5093184openalex-snapshot

Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components

inferred← citeshttps://doi.org/10.1063/1.5115085openalex-snapshot

Cell size effects in the molecular dynamics of the intrinsically disordered Aβ peptide

inferred← citeshttps://doi.org/10.1063/5.0101622openalex-snapshot

Impact of A2T and D23N mutations on C99 homodimer conformations

inferred← citeshttps://doi.org/10.1073/pnas.2023089118openalex-snapshot

Molecular structure of a prevalent amyloid-β fibril polymorph from Alzheimer's disease brain tissue

inferred← citeshttps://doi.org/10.1080/07391102.2019.1586587openalex-snapshot

Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations

inferred← citeshttps://doi.org/10.1080/07391102.2021.1939163openalex-snapshot

Modeling structural interconversion in Alzheimers’ amyloid beta peptide with classical and intrinsically disordered protein force fields

inferred← citeshttps://doi.org/10.1080/07391102.2023.2206917openalex-snapshot

Escherichia coli FtsZ molecular dynamics simulations

inferred← citeshttps://doi.org/10.1080/21690707.2017.1377813openalex-snapshot

How accurate are your simulations? Effects of confined aqueous volume and AMBER FF99SB and CHARMM22/CMAP force field parameters on structural ensembles of intrinsically disordered proteins: Amyloid-β42in water

inferred← citeshttps://doi.org/10.1080/23746149.2020.1770627openalex-snapshot

Molecular simulations of amyloid beta assemblies

inferred← citeshttps://doi.org/10.1088/2399-1984/abfb7copenalex-snapshot

Intrinsically disordered proteins at the nano-scale

inferred← citeshttps://doi.org/10.1101/2020.07.27.223487openalex-snapshot

Thermodynamics and kinetics of the amyloid-β peptide revealed by Markov state models based on MD data in agreement with experiment

inferred← citeshttps://doi.org/10.1101/2022.10.15.512345openalex-snapshot

Fast and Accurate Prediction of Intrinsically Disordered Protein by Protein Language Model

inferred← citeshttps://doi.org/10.1371/journal.pone.0205057openalex-snapshot

Ca2+ binding induced sequential allosteric activation of sortase A: An example for ion-triggered conformational selection

inferred← citeshttps://doi.org/10.18016/ksutarimdoga.vi.737200openalex-snapshot

Alpha-synuclein’ in PreNAC(46-56) Fibril Bölütünün Moleküler Dinamik Simülasyon Yöntemi ile Konformasyonel Değerlendirmesi

inferred← citeshttps://doi.org/10.2174/1567205017666201109094908openalex-snapshot

Current Challenges and Limitations in the Studies of Intrinsically Disordered Proteins in Neurodegenerative Diseases by Computer Simulations

inferred← citeshttps://doi.org/10.26434/chemrxiv-2021-4gg4gopenalex-snapshot

Modelling the structure and interactions of intrinsically disordered peptides with multiple-replica, metadynamics-based sampling methods and force-field combinations

inferred← citeshttps://doi.org/10.3233/jad-179902openalex-snapshot

Amyloid-β/Drug Interactions from Computer Simulations and Cell-Based Assays

inferred← citeshttps://doi.org/10.33774/chemrxiv-2021-4gg4g-v2openalex-snapshot

Modelling the structure and interactions of intrinsically disordered proteins with multiple-replica, metadynamics-based sampling methods and force-field combinations

inferred← citeshttps://doi.org/10.3389/fbioe.2019.00083openalex-snapshot

The Role of Structural Polymorphism in Driving the Mechanical Performance of the Alzheimer's Beta Amyloid Fibrils

inferred← citeshttps://doi.org/10.3390/biom15010028openalex-snapshot

Co-Localized in Amyloid Plaques Cathepsin B as a Source of Peptide Analogs Potential Drug Candidates for Alzheimer’s Disease

inferred← citeshttps://doi.org/10.3390/ijms19020336openalex-snapshot

Insights into the Molecular Mechanisms of Alzheimer’s and Parkinson’s Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology

inferred← citeshttps://doi.org/10.3390/ijms23116073openalex-snapshot

Allosteric Binding Sites of Aβ Peptides on the Acetylcholine Synthesizing Enzyme ChAT as Deduced by In Silico Molecular Modeling

inferred← citeshttps://doi.org/10.3390/ijms25031636openalex-snapshot

The Inhibition Effect of Epigallocatechin-3-Gallate on the Co-Aggregation of Amyloid-β and Human Islet Amyloid Polypeptide Revealed by Replica Exchange Molecular Dynamics Simulations

inferred← citeshttps://doi.org/10.3390/ijms25126698openalex-snapshot

A Practical Guide to All-Atom and Coarse-Grained Molecular Dynamics Simulations Using Amber and Gromacs: A Case Study of Disulfide-Bond Impact on the Intrinsically Disordered Amyloid Beta

inferred← citeshttps://doi.org/10.3390/molecules25153524openalex-snapshot

Fluorescence-Labeled Amyloid Beta Monomer: A Molecular Dynamical Study

inferred← citeshttps://doi.org/10.3390/ph18030306openalex-snapshot

Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics—Part A: Endogenous Compounds and Repurposed Drugs

inferred← citeshttps://doi.org/10.3390/ph18101457openalex-snapshot

Small-Molecule Inhibitors of Amyloid Beta: Insights from Molecular Dynamics—Part B: Natural Compounds

inferred← citeshttps://doi.org/10.3390/pharmaceutics15031018openalex-snapshot

Bacterial Lectin FimH and Its Aggregation Hot-Spots: An Alternative Strategy against Uropathogenic Escherichia coli

inferred← citeshttps://doi.org/10.3390/polym17152125openalex-snapshot

Complexation and Thermal Stabilization of Protein–Polyelectrolyte Systems via Experiments and Molecular Simulations: The Poly(acrylic acid)/Lysozyme Case

inferred← citeshttps://doi.org/10.70675/6f405727zb0adz4df8zbcbazc9a3c3451b97openalex-snapshot

Structure et dynamique de protéines intrinsèquement désordonnées : Caractérisation par une approche combinant dynamique moléculaire avancée et SAXS

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.