Chris Oostenbrink
Orcid: 0000-0002-4232-2556
According to our database1,
Chris Oostenbrink
authored at least 47 papers
between 2003 and 2023.
Collaborative distances:
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Bibliography
2023
Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene.
J. Chem. Inf. Model., November, 2023
Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from <i>Penaeus monodon</i>: An In Silico Study through MD Simulations.
J. Chem. Inf. Model., April, 2023
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom.
J. Chem. Inf. Model., 2023
2021
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family.
J. Chem. Inf. Model., 2021
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review.
J. Chem. Inf. Model., 2021
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins.
J. Comput. Chem., 2021
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2.
J. Comput. Aided Mol. Des., 2021
2020
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS).
J. Chem. Inf. Model., 2020
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field.
J. Chem. Inf. Model., 2020
Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies.
J. Comput. Chem., 2020
J. Comput. Chem., 2020
Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab.
BMC Bioinform., 2020
2019
GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations.
J. Chem. Inf. Model., 2019
2018
Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting.
J. Chem. Inf. Model., 2018
J. Comput. Chem., 2018
2017
J. Chem. Inf. Model., September, 2017
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field.
J. Comput. Chem., 2017
2016
Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting.
J. Chem. Inf. Model., 2016
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.
J. Comput. Chem., 2016
2015
Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14.
J. Chem. Inf. Model., 2015
2014
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation.
PLoS Comput. Biol., 2014
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.
J. Chem. Inf. Model., 2014
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides.
J. Chem. Inf. Model., 2014
J. Chem. Inf. Model., 2014
Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods.
J. Chem. Inf. Model., 2014
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies.
J. Comput. Chem., 2014
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.
J. Comput. Chem., 2014
J. Comput. Aided Mol. Des., 2014
2013
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications.
PLoS Comput. Biol., 2013
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies.
J. Comput. Chem., 2013
J. Comput. Chem., 2013
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase.
J. Comput. Aided Mol. Des., 2013
2012
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations.
J. Chem. Inf. Model., 2012
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants.
J. Chem. Inf. Model., 2012
J. Comput. Chem., 2012
2011
J. Comput. Chem., 2011
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase.
J. Comput. Chem., 2011
2010
J. Chem. Inf. Model., 2010
2009
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands.
J. Chem. Inf. Model., 2009
Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach.
J. Comput. Chem., 2009
2006
Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method.
J. Chem. Inf. Model., 2006
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.
J. Comput. Chem., 2006
2005
J. Comput. Chem., 2005
2004
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6.
J. Comput. Chem., 2004
2003
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character.
J. Comput. Chem., 2003