Chris Oostenbrink

Publication Activity (10 Years)

Years Active: 2003-2024
Publications (10 Years): 24

Top Topics

Molecular Dynamics

Protein Backbone

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

J. Comput. Aided Mol. Des.

Publications

Matic Broz, Chris Oostenbrink, Urban Bren
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J. Chem. Inf. Model. 64 (6) (2024)
Jakob Liu, Andreas Fischer, Monika Cserjan-Puschmann, Nico Lingg, Chris Oostenbrink
Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation. J. Chem. Inf. Model. 64 (14) (2024)
Oriol Gracia Carmona, Chris Oostenbrink
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. J. Chem. Inf. Model. 63 (1) (2023)
Mateo Barria-Urenda, Alvaro Ruiz-Fernandez, Carlos Gonzalez, Chris Oostenbrink, José Antonio Garate
Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J. Chem. Inf. Model. 63 (21) (2023)
Cristina González Fernández, Christoph Öhlknecht, Matthias Diem, Yerko Escalona, Eugenio Bringas, Gabriel Moncalián, Chris Oostenbrink, Inmaculada Ortiz
: An In Silico Study through MD Simulations. J. Chem. Inf. Model. 63 (8) (2023)
Christoph Öhlknecht, Sonja Katz, Christina Kröß, Bernhard Sprenger, Petra Engele, Rainer Schneider, Chris Oostenbrink
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family. J. Chem. Inf. Model. 61 (3) (2021)
Cristina González Fernández, Arantza Basauri, Marcos Fallanza, Eugenio Bringas, Chris Oostenbrink, Inmaculada Ortiz
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J. Chem. Inf. Model. 61 (10) (2021)
Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. 42 (18) (2021)
Jorge Enrique Hernández González, Emir Salas-Sarduy, Lilian Hernández Alvarez, Diego Enry Barreto Gomes, Pedro Geraldo Pascutti, Chris Oostenbrink, Vitor B. P. Leite
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J. Comput. Aided Mol. Des. 35 (10) (2021)
Bernhard Roither, Chris Oostenbrink, Wolfgang Schreiner
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. (17) (2020)
Jan Walther Perthold, Drazen Petrov, Chris Oostenbrink
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). J. Chem. Inf. Model. 60 (11) (2020)
Matthias Diem, Chris Oostenbrink
The effect of different cutoff schemes in molecular simulations of proteins. J. Comput. Chem. 41 (32) (2020)
Matthias Diem, Chris Oostenbrink
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. J. Chem. Inf. Model. 60 (1) (2020)
Christoph Öhlknecht, Bettina Lier, Drazen Petrov, Julian Fuchs, Chris Oostenbrink
Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. J. Comput. Chem. 41 (10) (2020)
Bernhard Roither, Chris Oostenbrink, Wolfgang Schreiner
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. BIBM (2019)
Jan Walther Perthold, Chris Oostenbrink
GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations. J. Chem. Inf. Model. 59 (12) (2019)
Christian Margreitter, Chris Oostenbrink
Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. 58 (8) (2018)
Manuela Maurer, Niels Hansen, Chris Oostenbrink
Comparison of free-energy methods using a tripeptide-water model system. J. Comput. Chem. 39 (26) (2018)
Aysegül Turupcu, Chris Oostenbrink
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes. J. Chem. Inf. Model. 57 (9) (2017)
Christian Margreitter, Maria M. Reif, Chris Oostenbrink
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. J. Comput. Chem. 38 (10) (2017)
Christian Margreitter, Chris Oostenbrink
MDplot: Visualise Molecular Dynamics. R J. 9 (1) (2017)
Michael M. H. Graf, Manuela Maurer, Chris Oostenbrink
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J. Comput. Chem. 37 (29) (2016)
Christian Margreitter, Chris Oostenbrink
Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. 56 (9) (2016)
Maria Pechlaner, Chris Oostenbrink
Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. J. Chem. Inf. Model. 55 (12) (2015)
Balder Lai, Gábor Nagy, José Antonio Garate, Chris Oostenbrink
Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods. J. Chem. Inf. Model. 54 (1) (2014)
Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. 10 (12) (2014)
Gábor Nagy, Chris Oostenbrink
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides. J. Chem. Inf. Model. 54 (1) (2014)
Ann-Beth Nørholm, Pierre Francotte, Eric Goffin, Iuliana Botez, Laurence Danober, Pierre Lestage, Bernard Pirotte, Jette S. Kastrup, Lars Olsen, Chris Oostenbrink
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. 54 (12) (2014)
Maria M. Reif, Chris Oostenbrink
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. J. Comput. Chem. 35 (32) (2014)
Gábor Nagy, Chris Oostenbrink
Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins. J. Chem. Inf. Model. 54 (1) (2014)
Eszter Németh, Gabriella K. Schilli, Gábor Nagy, Christoph Hasenhindl, Béla Gyurcsik, Chris Oostenbrink
Design of a colicin E7 based chimeric zinc-finger nuclease. J. Comput. Aided Mol. Des. 28 (8) (2014)
Maria M. Reif, Chris Oostenbrink
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J. Comput. Chem. 35 (3) (2014)
José Antonio Garate, Chris Oostenbrink
Free-energy differences between states with different conformational ensembles. J. Comput. Chem. 34 (16) (2013)
Michael M. H. Graf, Urban Bren, Dietmar Haltrich, Chris Oostenbrink
Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. J. Comput. Aided Mol. Des. 27 (4) (2013)
Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications. PLoS Comput. Biol. 9 (7) (2013)
Anita de Ruiter, Stefan Boresch, Chris Oostenbrink
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. J. Comput. Chem. 34 (12) (2013)
Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J. Comput. Chem. 33 (17) (2012)
Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. J. Chem. Inf. Model. 52 (8) (2012)
Urban Bren, Chris Oostenbrink
Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. J. Chem. Inf. Model. 52 (6) (2012)
Stephanie B. A. De Beer, Alice Glättli, Johannes Hutzler, Nico P. E. Vermeulen, Chris Oostenbrink
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. J. Comput. Chem. 32 (10) (2011)
Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren
Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. 32 (9) (2011)
Rita Santos, Jozef Hritz, Chris Oostenbrink
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. J. Chem. Inf. Model. 50 (1) (2010)
Chris Oostenbrink
Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach. J. Comput. Chem. 30 (2) (2009)
Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. J. Chem. Inf. Model. 49 (1) (2009)
Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen, Chris Oostenbrink
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. 46 (5) (2006)
Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan
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. 27 (7) (2006)
Markus Christen, Philippe H. Hünenberger, Dirk Bakowies, Riccardo Baron, Roland Bürgi, Daan P. Geerke, Tim N. Heinz, Mika A. Kastenholz, Vincent Kräutler, Chris Oostenbrink, Christine Peter, Daniel Trzesniak, Wilfred F. van Gunsteren
The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26 (16) (2005)
Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren
An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. 26 (7) (2005)
Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren
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. 25 (13) (2004)
Chris Oostenbrink, Wilfred F. van Gunsteren
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. 24 (14) (2003)