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Chris Oostenbrink
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2020 – today
- 2024
- [j50]Matic Broz
, Chris Oostenbrink
The Effect of Microwaves on Protein Structure: Molecular Dynamics Approach. J. Chem. Inf. Model. 64(6): 2077-2083 (2024) - [j49]Jakob Liu, Andreas Fischer, Monika Cserjan-Puschmann
Caspase-Based Fusion Protein Technology: Substrate Cleavability Described by Computational Modeling and Simulation. J. Chem. Inf. Model. 64(14): 5691-5700 (2024) - [j48]Wilfred F. van Gunsteren
Methods for Classical-Mechanical Molecular Simulation in Chemistry: Achievements, Limitations, Perspectives. J. Chem. Inf. Model. 64(16): 6281-6304 (2024) - 2023
- [j47]Oriol Gracia Carmona
Accelerated Enveloping Distribution Sampling (AEDS) Allows for Efficient Sampling of Orthogonal Degrees of Freedom. J. Chem. Inf. Model. 63(1): 197-207 (2023) - [j46]Cristina González Fernández
Insights into the Binding Mode of Lipid A to the Anti-lipopolysaccharide Factor ALFPm3 from Penaeus monodon: An In Silico Study through MD Simulations. J. Chem. Inf. Model. 63(8): 2495-2504 (2023) - [j45]Mateo Barria-Urenda
Size Matters: Free-Energy Calculations of Amino Acid Adsorption over Pristine Graphene. J. Chem. Inf. Model. 63(21): 6642-6654 (2023) - 2021
- [j44]Jorge Enrique Hernández González
In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. J. Comput. Aided Mol. Des. 35(10): 1067-1079 (2021) - [j43]Maria Pechlaner
On the use of multiple-time-step algorithms to save computing effort in molecular dynamics simulations of proteins. J. Comput. Chem. 42(18): 1263-1282 (2021) - [j42]Christoph Öhlknecht
Efficient In Silico Saturation Mutagenesis of a Member of the Caspase Protease Family. J. Chem. Inf. Model. 61(3): 1193-1203 (2021) - [j41]Cristina González Fernández
Fighting Against Bacterial Lipopolysaccharide-Caused Infections through Molecular Dynamics Simulations: A Review. J. Chem. Inf. Model. 61(10): 4839-4851 (2021) - 2020
- [j40]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. 21-S(17): 557 (2020) - [j39]Christoph Öhlknecht
Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. J. Comput. Chem. 41(10): 986-999 (2020) - [j38]Matthias Diem
The effect of different cutoff schemes in molecular simulations of proteins. J. Comput. Chem. 41(32): 2740-2749 (2020) - [j37]Matthias Diem
Hamiltonian Reweighing To Refine Protein Backbone Dihedral Angle Parameters in the GROMOS Force Field. J. Chem. Inf. Model. 60(1): 279-288 (2020) - [j36]Jan Walther Perthold
Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). J. Chem. Inf. Model. 60(11): 5395-5406 (2020)
2010 – 2019
- 2019
- [j35]Jan Walther Perthold
GroScore: Accurate Scoring of Protein-Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations. J. Chem. Inf. Model. 59(12): 5074-5085 (2019) - [c1]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: 2192-2196 - 2018
- [j34]Manuela Maurer, Niels Hansen
Comparison of free-energy methods using a tripeptide-water model system. J. Comput. Chem. 39(26): 2226-2242 (2018) - [j33]Christian Margreitter, Chris Oostenbrink
Correction to Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. 58(8): 1716-1720 (2018) - 2017
- [j32]Christian Margreitter
Update on phosphate and charged post-translationally modified amino acid parameters in the GROMOS force field. J. Comput. Chem. 38(10): 714-720 (2017) - [j31]Aysegül Turupcu
Modeling of Oligosaccharides within Glycoproteins from Free-Energy Landscapes. J. Chem. Inf. Model. 57(9): 2222-2236 (2017) - [j30]Christian Margreitter, Chris Oostenbrink:
MDplot: Visualise Molecular Dynamics. R J. 9(1): 164 (2017) - 2016
- [j29]Michael M. H. Graf, Manuela Maurer
Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling. J. Comput. Chem. 37(29): 2597-2605 (2016) - [j28]Christian Margreitter
Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J. Chem. Inf. Model. 56(9): 1823-1834 (2016) - 2015
- [j27]Maria Pechlaner
Multiple Binding Poses in the Hydrophobic Cavity of Bee Odorant Binding Protein AmelOBP14. J. Chem. Inf. Model. 55(12): 2633-2643 (2015) - 2014
- [j26]Eszter Németh, Gabriella K. Schilli, Gábor Nagy, Christoph Hasenhindl, Béla Gyurcsik
Design of a colicin E7 based chimeric zinc-finger nuclease. J. Comput. Aided Mol. Des. 28(8): 841-850 (2014) - [j25]Maria M. Reif
Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J. Comput. Chem. 35(3): 227-243 (2014) - [j24]Maria M. Reif
Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies. J. Comput. Chem. 35(32): 2319-2332 (2014) - [j23]Balder Lai
Entropic and Enthalpic Contributions to Stereospecific Ligand Binding from Enhanced Sampling Methods. J. Chem. Inf. Model. 54(1): 151-158 (2014) - [j22]Gábor Nagy, Chris Oostenbrink
Dihedral-Based Segment Identification and Classification of Biopolymers I: Proteins. J. Chem. Inf. Model. 54(1): 266-277 (2014) - [j21]Gábor Nagy, Chris Oostenbrink
Dihedral-Based Segment Identification and Classification of Biopolymers II: Polynucleotides. J. Chem. Inf. Model. 54(1): 278-288 (2014) - [j20]Ann-Beth Nørholm, Pierre Francotte
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): 3404-3416 (2014) - [j19]Michael M. H. Graf, Zhixiong Lin, Urban Bren, Dietmar Haltrich
Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation. PLoS Comput. Biol. 10(12) (2014) - 2013
- [j18]Michael M. H. Graf, Urban Bren, Dietmar Haltrich
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): 295-304 (2013) - [j17]Anita de Ruiter
Comparison of thermodynamic integration and Bennett's acceptance ratio for calculating relative protein-ligand binding free energies. J. Comput. Chem. 34(12): 1024-1034 (2013) - [j16]José Antonio Garate
Free-energy differences between states with different conformational ensembles. J. Comput. Chem. 34(16): 1398-1408 (2013) - [j15]Drazen Petrov
A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications. PLoS Comput. Biol. 9(7) (2013) - 2012
- [j14]Denise Steiner, Chris Oostenbrink
Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9. J. Comput. Chem. 33(17): 1467-1477 (2012) - [j13]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): 1573-1582 (2012) - [j12]Stephanie B. A. De Beer, Harini Venkataraman, Daan P. Geerke
Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants. J. Chem. Inf. Model. 52(8): 2139-2148 (2012) - 2011
- [j11]Denise Steiner, Chris Oostenbrink
Calculation of binding free energies of inhibitors to plasmepsin II. J. Comput. Chem. 32(9): 1801-1812 (2011) - [j10]Stephanie B. A. De Beer, Alice Glättli, Johannes Hutzler, Nico P. E. Vermeulen
Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase. J. Comput. Chem. 32(10): 2160-2169 (2011) - 2010
- [j9]Rita Santos
Role of Water in Molecular Docking Simulations of Cytochrome P450 2D6. J. Chem. Inf. Model. 50(1): 146-154 (2010)
2000 – 2009
- 2009
- [j8]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): 212-221 (2009) - [j7]Poongavanam Vasanthanathan
Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands. J. Chem. Inf. Model. 49(1): 43-52 (2009) - 2006
- [j6]Yu Zhou
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): 857-867 (2006) - [j5]Eva Stjernschantz, John Marelius, Carmen Medina, Micael Jacobsson, Nico P. E. Vermeulen
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): 1972-1983 (2006) - 2005
- [j4]Thereza A. Soares
An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. 26(7): 725-737 (2005) - [j3]Markus Christen, Philippe H. Hünenberger
The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26(16): 1719-1751 (2005) - 2004
- [j2]Chris Oostenbrink
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): 1656-1676 (2004) - 2003
- [j1]Chris Oostenbrink
Single-step perturbations to calculate free energy differences from unphysical reference states: Limits on size, flexibility, and character. J. Comput. Chem. 24(14): 1730-1739 (2003)
Coauthor Index
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last updated on 2024-10-07 22:16 CEST by the dblp team
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