Chris Oostenbrink

53 papers Journal 52Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Binding Site Vectors Enable Mapping of Cytochrome P450 Functional Landscapes. J. Chem. Inf. Model. Tea Kuvek, Zuzana Jandová, Klaus-Jürgen Schleifer, Chris Oostenbrink
2025	J	`jnl`	A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS. J. Comput. Chem. Peter Poliak, Patrick Bleiziffer, Felix Pultar, Sereina Riniker, Chris Oostenbrink
2024	J	`jnl`	Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation. J. Chem. Inf. Model. Jakob Liu, Andreas Fischer, Monika Cserjan-Puschmann, Nico Lingg, Chris Oostenbrink
2024	J	`jnl`	Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J. Chem. Inf. Model. Wilfred F. van Gunsteren, Chris Oostenbrink
2024	J	`jnl`	The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J. Chem. Inf. Model. Matic Broz, Chris Oostenbrink, Urban Bren
2023	J	`jnl`	Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. J. Chem. Inf. Model. Oriol Gracia Carmona, Chris Oostenbrink
2023	J	`jnl`	Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from J. Chem. Inf. Model. Cristina González Fernández, Christoph Öhlknecht, Matthias Diem, Yerko Escalona, Eugenio Bringas, Gabriel Moncalián, Chris Oostenbrink, Inmaculada Ortiz
2023	J	`jnl`	Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J. Chem. Inf. Model. Mateo Barria-Urenda, Alvaro Ruiz-Fernandez, Carlos Gonzalez, Chris Oostenbrink, José Antonio Garate
2021	J	`jnl`	Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family. J. Chem. Inf. Model. Christoph Öhlknecht, Sonja Katz, Christina Kröß, Bernhard Sprenger, Petra Engele, Rainer Schneider, Chris Oostenbrink
2021	J	`jnl`	Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J. Chem. Inf. Model. Cristina González Fernández, Arantza Basauri, Marcos Fallanza, Eugenio Bringas, Chris Oostenbrink, Inmaculada Ortiz
2021	J	`jnl`	In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J. Comput. Aided Mol. Des. Jorge Enrique Hernández González, Emir Salas-Sarduy, Lilian Hernández Alvarez, Diego Enry Barreto Gomes, Pedro Geraldo Pascutti, Chris Oostenbrink, Vitor B. P. Leite
2021	J	`jnl`	On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. Maria Pechlaner, Chris Oostenbrink, Wilfred F. van Gunsteren
2020	J	`jnl`	Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. J. Comput. Chem. Christoph Öhlknecht, Bettina Lier, Drazen Petrov, Julian Fuchs, Chris Oostenbrink
2020	J	`jnl`	Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. J. Chem. Inf. Model. Matthias Diem, Chris Oostenbrink
2020	J	`jnl`	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. Bernhard Roither, Chris Oostenbrink, Wolfgang Schreiner
2020	J	`jnl`	The effect of different cutoff schemes in molecular simulations of proteins. J. Comput. Chem. Matthias Diem, Chris Oostenbrink
2020	J	`jnl`	Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). J. Chem. Inf. Model. Jan Walther Perthold, Drazen Petrov, Chris Oostenbrink
2019	J	`jnl`	GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations. J. Chem. Inf. Model. Jan Walther Perthold, Chris Oostenbrink
2019	—	`conf`	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 Bernhard Roither, Chris Oostenbrink, Wolfgang Schreiner
2018	J	`jnl`	Comparison of free-energy methods using a tripeptide-water model system. J. Comput. Chem. Manuela Maurer, Niels Hansen, Chris Oostenbrink
2018	J	`jnl`	Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. Christian Margreitter, Chris Oostenbrink
2017	J	`jnl`	MDplot: Visualise Molecular Dynamics. R J. Christian Margreitter, Chris Oostenbrink
2017	J	`jnl`	Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes. J. Chem. Inf. Model. Aysegül Turupcu, Chris Oostenbrink
2017	J	`jnl`	Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. J. Comput. Chem. Christian Margreitter, Maria M. Reif, Chris Oostenbrink
2016	J	`jnl`	Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J. Comput. Chem. Michael M. H. Graf, Manuela Maurer, Chris Oostenbrink
2016	J	`jnl`	Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. Christian Margreitter, Chris Oostenbrink
2015	J	`jnl`	Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. J. Chem. Inf. Model. Maria Pechlaner, Chris Oostenbrink
2014	J	`jnl`	Design of a colicin E7 based chimeric zinc-finger nuclease. J. Comput. Aided Mol. Des. Eszter Németh, Gabriella K. Schilli, Gábor Nagy, Christoph Hasenhindl, Béla Gyurcsik, Chris Oostenbrink
2014	J	`jnl`	Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins. J. Chem. Inf. Model. Gábor Nagy, Chris Oostenbrink
2014	J	`jnl`	Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides. J. Chem. Inf. Model. Gábor Nagy, Chris Oostenbrink
2014	J	`jnl`	Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods. J. Chem. Inf. Model. Balder Lai, Gábor Nagy, José Antonio Garate, Chris Oostenbrink
2014	J	`jnl`	Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. J. Comput. Chem. Maria M. Reif, Chris Oostenbrink
2014	J	`jnl`	Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J. Comput. Chem. Maria M. Reif, Chris Oostenbrink
2014	J	`jnl`	Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich, Wilfred F. van Gunsteren, Chris Oostenbrink
2014	J	`jnl`	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. Ann-Beth Nørholm, Pierre Francotte, Eric Goffin, Iuliana Botez, Laurence Danober, Pierre Lestage, Bernard Pirotte, Jette S. Kastrup, Lars Olsen, Chris Oostenbrink
2013	J	`jnl`	A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications. PLoS Comput. Biol. Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic
2013	J	`jnl`	Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. J. Comput. Chem. Anita de Ruiter, Stefan Boresch, Chris Oostenbrink
2013	J	`jnl`	Free-energy differences between states with different conformational ensembles. J. Comput. Chem. José Antonio Garate, Chris Oostenbrink
2013	J	`jnl`	Molecular dynamics simulations give insight into d-glucose dioxidation at C2 and C3 by Agaricus meleagris pyranose dehydrogenase. J. Comput. Aided Mol. Des. Michael M. H. Graf, Urban Bren, Dietmar Haltrich, Chris Oostenbrink
2012	J	`jnl`	Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J. Comput. Chem. Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren
2012	J	`jnl`	Cytochrome P450 3A4 Inhibition by Ketoconazole: Tackling the Problem of Ligand Cooperativity Using Molecular Dynamics Simulations and Free-Energy Calculations. J. Chem. Inf. Model. Urban Bren, Chris Oostenbrink
2012	J	`jnl`	Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. J. Chem. Inf. Model. Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke, Chris Oostenbrink, Nico P. E. Vermeulen
2011	J	`jnl`	Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren
2011	J	`jnl`	Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. J. Comput. Chem. Stephanie B. A. De Beer, Alice Glättli, Johannes Hutzler, Nico P. E. Vermeulen, Chris Oostenbrink
2010	J	`jnl`	Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. J. Chem. Inf. Model. Rita Santos, Jozef Hritz, Chris Oostenbrink
2009	J	`jnl`	Efficient free energy calculations on small molecule host-guest systems - A combined linear interaction energy/one-step perturbation approach. J. Comput. Chem. Chris Oostenbrink
2009	J	`jnl`	Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. J. Chem. Inf. Model. Poongavanam Vasanthanathan, Jozef Hritz, Olivier Taboureau, Lars Olsen, Flemming Steen Jørgensen, Nico P. E. Vermeulen, Chris Oostenbrink
2006	J	`jnl`	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. Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen, Chris Oostenbrink
2006	J	`jnl`	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. Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan
2005	J	`jnl`	An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren
2005	J	`jnl`	The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 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
2004	J	`jnl`	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. Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. van Gunsteren
2003	J	`jnl`	Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. Chris Oostenbrink, Wilfred F. van Gunsteren