List of works - Birgit Strodel

A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly

scientific article published on 17 January 2014

Advances in the Simulation of Protein Aggregation at the Atomistic Scale.

scientific article published on 10 March 2016

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

scientific article

Amyloid-β Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects

scientific article published on 04 May 2018

An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations

scientific article published on 22 February 2016

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

scientific article published on 01 March 2019

Aβ under stress: the effects of acidosis, Cu2+-binding, and oxidation on amyloid β-peptide dimers

scientific article published in 2018

Biochemical and structural characterization of murine GBP7, a guanylate binding protein with an elongated C-terminal tail

scientific article published on 01 November 2019

Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease

scientific article

Characterizing the first steps of amyloid formation for the ccbeta peptide

scientific article

Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study

scientific article published on 17 March 2018

Classical Calculation of Transient Absorption Spectra Monitoring Ultrafast Electron Transfer Processes

scientific article published on 21 October 2006

Conformational Polymorphism in Autophagy-Related Protein GATE-16

scientific article

Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect

scientific article published on 18 June 2015

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

scientific article published on 11 November 2020

Early amyloid β-protein aggregation precedes conformational change

scientific article published in 2014

Effects of in vivo conditions on amyloid aggregation

scientific article published on 01 July 2019

Evaluation of the coarse-grained OPEP force field for protein-protein docking.

scientific article

Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions

scientific article published on 12 October 2017

Extension of the FACTS Implicit Solvation Model to Membranes.

scientific article published on 11 June 2014

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2

scientific article published on 13 July 2020

Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide

scientific article published on 14 March 2008

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

scientific article published on 08 January 2019

Interaction of Bcl-2 with the autophagy-related GABAA receptor-associated protein (GABARAP): biophysical characterization and functional implications.

scientific article published on 15 November 2013

Interference with Amyloid-β Nucleation by Transient Ligand Interaction

scientific article published on 05 June 2019

Interpolation schemes for peptide rearrangements

scientific article published in February 2010

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

scientific article published on 07 October 2019

Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case

scholarly article by Qinghua Liao et al published 8 November 2018 in Journal of the American Chemical Society

Markov models for the elucidation of allosteric regulation

scientific article published on 19 June 2018

Membrane permeation induced by aggregates of human islet amyloid polypeptides

scientific article

Modelling proteins: conformational sampling and reconstruction of folding kinetics.

scientific article published on 17 September 2010

Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex.

scientific article published on 7 August 2017

Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 fromWuchereria bancroftiusing cheminformatics and mutational studies

scientific article published in July 2013

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

scientific article

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

scientific article published on 31 October 2018

Pathways of Amyloid-β Aggregation Depend on Oligomer Shape.

scientific article published on 13 December 2017

Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data

scientific article published on 24 November 2020

Protein structure prediction using global optimization by basin-hopping with NMR shift restraints ⬇️

scientific article published on January 14, 2013

Protein structure prediction: assembly of secondary structure elements by basin-hopping.

scientific article

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics

scientific article published in March 2006

Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide

scientific article

Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease

scientific article published on 12 December 2019

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

scientific article published on 30 January 2020

Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase

scientific article published in August 2017

Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation

scientific article published on 9 March 2018

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site

scientific article published on 02 October 2019

Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations.

scientific article published on 7 November 2013

Structural features determining thermal adaptation of esterases.

scientific article

Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation

scientific article published on 3 May 2018

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

scientific article published in March 2012

Symmetrization of the AMBER and CHARMM force fields.

scientific article published in May 2010

Thermodynamic analysis of structural transitions during GNNQQNY aggregation

scientific article published on 12 April 2013

Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

scientific article published in December 2007

Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22

scientific article

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

scientific article published on 15 April 2019

Transmembrane structures for Alzheimer's Aβ(1-42) oligomers.

scientific article

Understanding Amyloid-β Oligomerization at the Molecular Level: The Role of the Fibril Surface

scientific article published on 24 May 2016

List of works by Birgit Strodel

A kinetic approach to the sequence-aggregation relationship in disease-related protein assembly

Advances in the Simulation of Protein Aggregation at the Atomistic Scale.

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

Amyloid-β Peptide Interactions with Amphiphilic Surfactants: Electrostatic and Hydrophobic Effects

An Account of Amyloid Oligomers: Facts and Figures Obtained from Experiments and Simulations

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

Aβ under stress: the effects of acidosis, Cu2+-binding, and oxidation on amyloid β-peptide dimers

Biochemical and structural characterization of murine GBP7, a guanylate binding protein with an elongated C-terminal tail

Characterization of Mn(II) ion binding to the amyloid-β peptide in Alzheimer's disease

Characterizing the first steps of amyloid formation for the ccbeta peptide

Cholesterol Protects the Oxidized Lipid Bilayer from Water Injury: An All-Atom Molecular Dynamics Study

Classical Calculation of Transient Absorption Spectra Monitoring Ultrafast Electron Transfer Processes

Conformational Polymorphism in Autophagy-Related Protein GATE-16

Development and Application of a Nonbonded Cu(2+) Model That Includes the Jahn-Teller Effect

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

Early amyloid β-protein aggregation precedes conformational change

Effects of in vivo conditions on amyloid aggregation

Evaluation of the coarse-grained OPEP force field for protein-protein docking.

Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions

Extension of the FACTS Implicit Solvation Model to Membranes.

High Throughput Virtual Screening to Discover Inhibitors of the Main Protease of the Coronavirus SARS-CoV-2

Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide

Integrated NMR, Fluorescence, and Molecular Dynamics Benchmark Study of Protein Mechanics and Hydrodynamics

Interaction of Bcl-2 with the autophagy-related GABAA receptor-associated protein (GABARAP): biophysical characterization and functional implications.

Interference with Amyloid-β Nucleation by Transient Ligand Interaction

Interpolation schemes for peptide rearrangements

Large-scale, dynamin-like motions of the human guanylate binding protein 1 revealed by multi-resolution simulations

Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case

Markov models for the elucidation of allosteric regulation

Membrane permeation induced by aggregates of human islet amyloid polypeptides

Modelling proteins: conformational sampling and reconstruction of folding kinetics.

Molecular Dynamics Simulations Reveal Key Roles of the Interleukin-6 Alpha Receptor in the Assembly of the Human Interleukin-6 Receptor Complex.

Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 fromWuchereria bancroftiusing cheminformatics and mutational studies

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

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

Pathways of Amyloid-β Aggregation Depend on Oligomer Shape.

Performance of Markov State Models and Transition Networks on Characterizing Amyloid Aggregation Pathways from MD Data

Protein structure prediction using global optimization by basin-hopping with NMR shift restraints ⬇️

Protein structure prediction: assembly of secondary structure elements by basin-hopping.

Quantum modeling of transient infrared spectra reflecting photoinduced electron-transfer dynamics

Radical Formation Initiates Solvent-Dependent Unfolding and β-sheet Formation in a Model Helical Peptide

Rational Drug Design of Peptide-Based Therapies for Sickle Cell Disease

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

Shuffling Active Site Substate Populations Affects Catalytic Activity: The Case of Glucose Oxidase

Simulation-Guided Design of Cytochrome P450 for Chemo- and Regioselective Macrocyclic Oxidation

Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site

Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations.

Structural features determining thermal adaptation of esterases.

Structural insights from lipid-bilayer nanodiscs link α-Synuclein membrane-binding modes to amyloid fibril formation

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

Symmetrization of the AMBER and CHARMM force fields.

Thermodynamic analysis of structural transitions during GNNQQNY aggregation

Thermodynamics and Kinetics of Aggregation for the GNNQQNY Peptide

Topology and parameter data of thirteen non-natural amino acids for molecular simulations with CHARMM22

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

Transmembrane structures for Alzheimer's Aβ(1-42) oligomers.

Understanding Amyloid-β Oligomerization at the Molecular Level: The Role of the Fibril Surface