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List of works by Chris Oostenbrink

A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field

scientific article published on 21 January 2003

A library of fluorescent peptides for exploring the substrate specificities of prolyl isomerases

scientific article

A pH Replica Exchange Scheme in the Stochastic Titration Constant-pH MD Method

scientific article published on 03 April 2019

A speculation on the tandem fasciclin 1 repeat of FLA4 proteins in angiosperms

scientific article published on 27 August 2018

A stereochemical switch in the aDrs model system, a candidate for a functional amyloid

scientific article

A systematic framework for molecular dynamics simulations of protein post-translational modifications

scientific article

Accelerated Enveloping Distribution Sampling: Enabling Sampling of Multiple End-States While Preserving Local Energy Minima

scientific article published on 18 April 2018

Actinobacterial Coproheme Decarboxylases Use Histidine as a Distal Base to Promote Compound I Formation

scientific article published on 09 April 2020

Amine hydration: a united-atom force-field solution

scientific article published in September 2005

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

scientific article published on 15 November 2011

An improved nucleic acid parameter set for the GROMOS force field

Anti-endotoxic activity and structural basis for human MD-2·TLR4 antagonism of tetraacylated lipid A mimetics based on βGlcN(1↔1)αGlcN scaffold

scientific article

Antibody humanization by molecular dynamics simulations-in-silico guided selection of critical backmutations

scientific article published on 8 January 2016

Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method

article

Bestimmung von Strukturinformation aus experimentellen Messdaten für Biomoleküle

article

Binding Modes and Metabolism of Caffeine

scientific article published on 11 June 2019

Binding free energy, energy and entropy calculations using simple model systems

article

Binding of 7-methoxy-4-(aminomethyl)-coumarin to wild-type and W128F mutant cytochrome P450 2D6 studied by time-resolved fluorescence spectroscopy

scientific article published in February 2006

Biomolecular modeling: Goals, problems, perspectives

scientific article published on June 2006

Biophysical and physicochemical methods differentiate highly ligand-efficient human D-amino acid oxidase inhibitors.

scientific article published on 13 May 2011

CHAPTER 4. Cytochrome P450 Mediated Drug Metabolism

CYP 2D6 binding affinity predictions using multiple ligand and protein conformations

scientific article published on 17 December 2013

Calculating zeros: Non-equilibrium free energy calculations

Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

scientific article

Calculation of Relative Free Energies for Ligand-Protein Binding, Solvation, and Conformational Transitions Using the GROMOS Software

scholarly article by Sereina Riniker et al published 24 November 2011 in Journal of Physical Chemistry

Calculation of binding free energies of inhibitors to plasmepsin II.

scientific article published on 12 April 2011

Calculation of substrate binding affinities for a bacterial GH78 rhamnosidase through molecular dynamics simulations

scientific article published on August 2013

Calculation of the Redox Potential of the Protein Azurin and Some Mutants

scientific article published in 2005

Calculation of the relative free energy of oxidation of Azurin at pH 5 and pH 9.

scientific article published on 24 April 2012

Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ

scientific article published on 18 June 2010

Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking.

scientific article published in April 2006

Cellular levels and molecular dynamics simulations of estragole DNA adducts point at inefficient repair resulting from limited distortion of the double-stranded DNA helix

scientific article published on 18 March 2020

Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems

scientific article published on 02 November 2020

Chemical Approach to Biological Safety: Molecular-Level Control of an Integrated Zinc Finger Nuclease.

scientific article

Chemistry and Molecular Dynamics Simulations of Heme b-HemQ and Coproheme-HemQ.

scientific article

Classification of cytochrome P450 1A2 inhibitors and noninhibitors by machine learning techniques.

scientific article

Comparison of free-energy methods using a tripeptide-water model system

article

Comparison of murine and human estrogen sulfotransferase inhibition in vitro and in silico--implications for differences in activity, subunit dimerization and substrate inhibition

scientific article published on 16 December 2009

Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies

scientific article published on 19 January 2013

Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

scientific article

Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450

scientific article published on 01 May 2008

Computational study of ground-state chiral induction in small peptides: Comparison of the relative stability of selected amino acid dimers and oligomers in homochiral and heterochiral combinations

scientific article published on 01 May 2006

Configurational entropy change of netropsin and distamycin upon DNA minor-groove binding

scientific article

Conformationally constrained lipid A mimetics for exploration of structural basis of TLR4/MD-2 activation by lipopolysaccharide

scientific article published on 26 September 2013

Construction of pH-sensitive Her2-binding IgG1-Fc by directed evolution

scientific article

Cooperative binding of aflatoxin B1 by cytochrome P450 3A4: a computational study

scientific article published on 26 November 2014

Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies

scientific article published on 12 January 2020

Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

scholarly article published in Journal of Chemical Information and Modeling

Could Microwave Irradiation Cause Misfolding of Peptides?

scientific article published on 20 March 2020

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

scientific article

Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations

article

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

scientific article

Design of a colicin E7 based chimeric zinc-finger nuclease

scientific article

Dihedral-based segment identification and classification of biopolymers I: proteins

scientific article published on 10 January 2014

Dihedral-based segment identification and classification of biopolymers II: polynucleotides

scientific article

Efficient Calculation of Many Stacking and Pairing Free Energies in DNA from a Few Molecular Dynamics Simulations

article

Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors

scientific article published on 3 February 2012

Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

scientific article published in September 2009

Efficient free energy calculations on small molecule host-guest systems - a combined linear interaction energy/one-step perturbation approach

scientific article published in January 2009

Enhancing the promiscuity of a member of the Caspase protease family by rational design

scientific article published on 20 May 2020

Entropic and enthalpic contributions to stereospecific ligand binding from enhanced sampling methods

scientific article published on 9 January 2014

Estimating entropies from molecular dynamics simulations

article

Eukaryotic Catalase-Peroxidase: The Role of the Trp-Tyr-Met Adduct in Protein Stability, Substrate Accessibility, and Catalysis of Hydrogen Peroxide Dismutation

scientific article

Exploring genetic suppression interactions on a global scale

scientific article

Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints

scientific article

Expression and glycoengineering of functionally active heteromultimeric IgM in plants

scientific article

Extended Thermodynamic Integration: Efficient Prediction of Lambda Derivatives at Nonsimulated Points

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

scholarly article by Patrik Rydberg et al published 30 November 2009 in ChemMedChem

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants

scientific article published on 19 July 2012

Free Energy Calculations from One-Step Perturbations ⬇️

article by Chris Oostenbrink published 24 November 2011 in Methods in Molecular Biology

Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations

scientific article published on 27 February 2007

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

scientific article published in February 2004

Free energies of ligand binding for structurally diverse compounds

scientific article

Free energy calculations of protein-ligand interactions

scientific article published on 22 June 2011

Free energy calculations on the stability of the 14-3-3ζ protein

scientific article

Free-Energy Calculations for Bioisosteric Modifications of A3 Adenosine Receptor Antagonists

scientific article published on 16 July 2019

Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling

scientific article (publication date: 5 November 2016)

Free-energy differences between states with different conformational ensembles

scientific article

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

scientific article published on 16 September 2011

GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations

scientific article published on 12 December 2019

Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field

scientific article published on 09 January 2020

Hamiltonian replica exchange molecular dynamics using soft-core interactions

scientific article published in April 2008

Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening

Identification of Critical Residues in Novel Drug Metabolizing Mutants of Cytochrome P450 BM3 Using Random Mutagenesis

scientific article published on 01 February 2007

Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking.

scientific article

Improved ligand-protein binding affinity predictions using multiple binding modes

scientific article

Improved spectrophotometric assay for lytic polysaccharide monooxygenase

scientific article published on 05 December 2019

Influence of Lytic Polysaccharide Monooxygenase Active Site Segments on Activity and Affinity ⬇️

scientific article published on 10 December 2019

Insights into structural features determining odorant affinities to honey bee odorant binding protein 14.

scientific article published on 21 March 2014

Interaction between Cellobiose Dehydrogenase and Lytic Polysaccharide Monooxygenase

scientific article published on 15 February 2019

Interaction with the Redox Cofactor MYW and Functional Role of a Mobile Arginine in Eukaryotic Catalase-Peroxidase

scientific article published on 13 June 2016

Investigation of ion binding in chlorite dismutases by means of molecular dynamics simulations

scientific article published on 14 July 2014

Ion-induced modification of the sucrose network and its impact on melting of freeze-dried liposomes. DSC and molecular dynamics study

scientific article published on 24 November 2017

Lipid A from lipopolysaccharide recognition: structure, dynamics and cooperativity by molecular dynamics simulations.

scientific article published on 15 January 2013

Malleability and Versatility of Cytochrome P450 Active Sites Studied by Molecular Simulations

scientific article published on 01 February 2012

Metabolic regio- and stereoselectivity of cytochrome P450 2D6 towards 3,4-methylenedioxy-N-alkylamphetamines: in silico predictions and experimental validation.

scientific article

Methane clustering in explicit water: effect of urea on hydrophobic interactions

scientific article published in January 2005

Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes.

scientific article

Molecular Conformations of Di-, Tri-, and Tetra-α-(2→8)-Linked Sialic Acid from NMR Spectroscopy and MD Simulations

scientific article published on 19 December 2019

Molecular Dynamics Simulations of the Standard Leonardite Humic Acid: Microscopic Analysis of the Structure and Dynamics

scientific article published on 25 April 2017

Molecular Insight into Propeptide–Protein Interactions in Cathepsins L and O ⬇️

scientific article published on October 16, 2012

Molecular Modeling-Guided Site-Directed Mutagenesis of Cytochrome P450 2D6

article

Molecular Simulations to Rationalize Humanized Ab2/3H6 Activity

Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

scientific article

Molecular dynamics simulation of the crystallizable fragment of IgG1-insights for the design of Fcabs

scientific article published on 2 January 2014

Molecular dynamics simulations

scientific article

Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site

scientific article

Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase

article

Molecular dynamics simulations give insight into D-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase

scientific article published on 17 April 2013

Molecular dynamics simulations give insight into the conformational change, complex formation, and electron transfer pathway for cytochrome P450 reductase

scientific article

Molecular dynamics simulations of the auxin-binding protein 1 in complex with indole-3-acetic acid and naphthalen-1-acetic acid

scientific article published on 17 July 2014

Molecular mechanism of allosteric communication in the human PPARalpha-RXRalpha heterodimer

scientific article published on March 2010

Molecular modelling of sorption processes of a range of diverse small organic molecules in Leonardite humic acid

scientific article published on 20 August 2019

Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14.

scientific article published on 3 December 2015

Mutations Increasing Cofactor Affinity, Improve Stability and Activity of a Baeyer–Villiger Monooxygenase

scientific article published in 2022

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation

scientific article published on 19 November 2013

New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field

scientific article published on 24 May 2012

On the thermodynamics of carbon nanotube single-file water loading: free energy, energy and entropy calculations

scientific article

On the transferability of the SPC/L water model to biomolecular simulation

article

On the use of multiple‐time‐step algorithms to save computing effort in molecular dynamics simulations of proteins

scientific article published on 06 May 2021

On the use of one-step perturbation to investigate the dependence of NOE-derived atom-atom distance bound violations of peptides upon a variation of force-field parameters

scientific article published on 7 February 2014

On using oscillating time-dependent restraints in MD simulation

scientific article published on 16 December 2006

Optimization of Alchemical Pathways Using Extended Thermodynamic Integration

scientific article published on 22 December 2020

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

scientific article

Optimization of replica exchange molecular dynamics by fast mimicking

scientific article published in November 2007

Pembrolizumab Induces an Unexpected Conformational Change in the CC'-loop of PD-1

scientific article published on 22 December 2020

Plasmon Field-Enhanced Fluorescence Energy Transfer for Hairpin Aptamer Assay Readout.

scientific article published on 6 July 2017

Polarization Effects in Simulations of Kaolinite-Water Interfaces

scientific article published on 12 November 2019

Prediction of cytochrome P450 mediated metabolism

scientific article published on 06 May 2015

Processing of complex N-glycans in IgG Fc-region is affected by core fucosylation

scientific article

Production of Circularly Permuted Caspase-2 for Affinity Fusion-Tag Removal: Cloning, Expression in <i>Escherichia coli</i>, Purification, and Characterization

scientific article published on 24 November 2020

Protein Conformational Change Is Essential for Reductive Activation of Lytic Polysaccharide Monooxygenase by Cellobiose Dehydrogenase

scientific article published on 30 March 2020

Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations

scientific article published on 10 January 2013

Pyranose dehydrogenase ligand promiscuity: a generalized approach to simulate monosaccharide solvation, binding, and product formation

scientific article

Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations

scientific article published on 20 October 2012

Reaction of pyranose dehydrogenase from Agaricus meleagris with its carbohydrate substrates

scientific article published on 18 August 2015

Recombinant plant-derived human IgE glycoproteomics

scientific article published on 8 April 2017

Redox Cofactor Rotates during Its Stepwise Decarboxylation: Molecular Mechanism of Conversion of Coproheme to Heme b

scientific article published on 18 June 2019

Redox thermodynamics of high-spin and low-spin forms of chlorite dismutases with diverse subunit and oligomeric structures

scientific article

Relative stability of homochiral and heterochiral dialanine peptides. Effects of perturbation pathways and force-field parameters on free energy calculations

Reparametrisation of united-atom amine solvation in the GROMOS force field

Role of water in molecular docking simulations of cytochrome P450 2D6.

scientific article published in January 2010

Saturation Mutagenesis by Efficient Free-Energy Calculation

scientific article published on 20 December 2017

Selectivity of cytosolic phospholipase A2 type IV toward arachidonyl phospholipids

scientific article published on 23 February 2015

Simulating the Physiological Phase of Hydrated DPPC Bilayers: The Ester Moiety

Simulation of Reversible Protein-Protein Binding and Calculation of Binding Free Energies Using Perturbed Distance Restraints

scientific article published on 12 September 2017

Simulations of the Estrogen Receptor Ligand-Binding Domain: Affinity of Natural Ligands and Xenoestrogens

article

Single-step perturbations to calculate free energy differences from unphysical reference states: limits on size, flexibility, and character

scientific article published in November 2003

Structural Aspects of the O-glycosylation Linkage in Glycopeptides via MD Simulations and Comparison with NMR Experiments.

scientific article published on 6 May 2019

Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3.

scientific article published in April 2008

Structure of human promyeloperoxidase (proMPO) and the role of the propeptide in processing and maturation

scientific article

Structure-Based Methods for Predicting the Sites and Products of Metabolism

Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins

scientific article

The GROMOS software for biomolecular simulation: GROMOS05.

scientific article

The effect of different cutoff schemes in molecular simulations of proteins

scientific article published on 07 October 2020

The impact of using single atomistic long range cutoff schemes with the GROMOS 54A7 force field

The role of water molecules in computational drug design

scientific article published on January 2010

Thermodynamic characterization of new positive allosteric modulators binding to the glutamate receptor A2 ligand-binding domain: combining experimental and computational methods unravels differences in driving forces

scientific article published on 9 December 2014

Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization

scientific article published on 10 January 2015

Transiently produced hypochlorite is responsible for the irreversible inhibition of chlorite dismutase

scientific article

Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface

scientific article published on 12 August 2013

UDP-sulfoquinovose formation by Sulfolobus acidocaldarius.

scientific article published on 21 January 2015

Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field

scientific article published on 24 January 2017

Validation of Molecular Simulation: An Overview of Issues

scientific article

Validation of the 53A6 GROMOS force field

scientific article

Validation of the GROMOS force-field parameter set 45Alpha3 against nuclear magnetic resonance data of hen egg lysozyme.

scientific article

Vienna Soil-Organic-Matter Modeler--Generating condensed-phase models of humic substances

scientific article published on 19 October 2015

Vienna soil organic matter modeler 2 (VSOMM2)

scientific article published on 26 November 2020

Virtual screening and prediction of site of metabolism for cytochrome P450 1A2 ligands.

scientific article

Water in protein hydration and ligand recognition

scientific article published on 27 August 2019

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