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1

Molecular dynamics simulations of the standard Leonardite humic acid: microscopic analysis of the structure and dynamics

Petrov, Drazen, Tunega, Daniel, Gerzabek, Martin H., Oostenbrink, Chris

Journal:

Environmental Science & Technology

Year:

2017

Language:

english

File:

PDF, 3.42 MB

english, 2017

2

A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6

Chris Oostenbrink, Alessandra Villa, Alan E. Mark, Wilfred F. Van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 181 KB

english, 2004

3

The GROMOS software for biomolecular simulation: GROMOS05

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 Tr

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 832 KB

english, 2005

4

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

Stephanie B. A. De Beer, Alice GlÄttli, Johannes Hutzler, Nico P. E. Vermeulen, Chris Oostenbrink

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 382 KB

english, 2011

5

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

Stjernschantz, Eva, Marelius, John, Medina, Carmen, Jacobsson, Micael, Vermeulen, Nico P. E., Oostenbrink, Chris

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 438 KB

english, 2006

6

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

Reif, Maria M., Mach, Lukas, Oostenbrink, Chris

Journal:

Year:

2012

Language:

english

File:

PDF, 3.74 MB

english, 2012

7

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

Perthold, Jan Walther, Oostenbrink, Chris

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 654 KB

english, 2018

8

Germinality does not necessarily define mAb expression and thermal stability

Schwaigerlehner, Linda, Mayrhofer, Patrick, Diem, Matthias, Steinfellner, Willibald, Fenech, Emma, Oostenbrink, Chris, Kunert, Renate

Journal:

Applied Microbiology and Biotechnology

Year:

2019

Language:

english

File:

PDF, 1.80 MB

english, 2019

9

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

Jandova, Zuzana, Jespers, Willem, Sotelo, Eddy, Gutiérrez-de-Terán, Hugo, Oostenbrink, Chris

Journal:

International Journal of Molecular Sciences

Year:

2019

Language:

english

File:

PDF, 2.64 MB

english, 2019

10

Could Microwave Irradiation Cause Misfolding of Peptides?

GladoviÄ, Martin, Oostenbrink, Chris, Bren, Urban

Journal:

Journal of Chemical Theory and Computation

Year:

2020

Language:

english

File:

PDF, 9.71 MB

english, 2020

11

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

Marieke van den Bosch, Marcel Swart, Jaap G. Snijders†, Herman J. C. Berendsen, Alan E. Mark, Chris Oostenbrink, Wilfred F. van Gunsteren, Gerard W. Canters

Journal:

Year:

2005

Language:

english

File:

PDF, 275 KB

english, 2005

12

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

Patrik Rydberg, Poongavanam Vasanthanathan, Chris Oostenbrink, Lars Olsen

Journal:

Year:

2009

Language:

english

File:

PDF, 338 KB

english, 2009

13

Fast Prediction of Cytochrome P450 Mediated Drug Metabolism

Patrik Rydberg, Poongavanam Vasanthanathan, Chris Oostenbrink, Lars Olsen

Journal:

Year:

2009

File:

PDF, 55 KB

2009

14

Amine Hydration: A United-Atom Force-Field Solution

Chris Oostenbrink, Daniel Juchli, Wilfred F. van Gunsteren

Journal:

Year:

2005

Language:

english

File:

PDF, 91 KB

english, 2005

15

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

Chris Oostenbrink, Wilfred F. Van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 183 KB

english, 2003

16

An improved nucleic acid parameter set for the GROMOS force field

Thereza A. Soares, Philippe H. Hünenberger, Mika A. Kastenholz, Vincent Kräutler, Thomas Lenz, Roberto D. Lins, Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 274 KB

english, 2005

17

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

Yu Zhou, Chris Oostenbrink, Aldo Jongejan, Wilfred F. Van Gunsteren, Wilfred R. Hagen, Simon W. De Leeuw, Jaap A. Jongejan

Journal:

Journal of Computational Chemistry

Year:

2006

Language:

english

File:

PDF, 535 KB

english, 2006

18

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

Chris Oostenbrink

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 184 KB

english, 2009

19

Calculation of binding free energies of inhibitors to plasmepsin II

Denise Steiner, Chris Oostenbrink, François Diederich, Martina Zürcher, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2011

Language:

english

File:

PDF, 783 KB

english, 2011

20

Free energy calculations of protein–ligand interactions

Anita de Ruiter, Chris Oostenbrink

Journal:

Current Opinion in Chemical Biology

Year:

2011

Language:

english

File:

PDF, 306 KB

english, 2011

21

Calculating zeros: Non-equilibrium free energy calculations

Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Chemical Physics

Year:

2006

Language:

english

File:

PDF, 225 KB

english, 2006

22

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

Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2004

Language:

english

File:

PDF, 363 KB

english, 2004

23

Structural rationalization of novel drug metabolizing mutants of cytochrome P450 BM3

Eva Stjernschantz, Barbara M. A. van Vugt-Lussenburg, Alois Bonifacio, Stephanie B. A. de Beer, Gert van der Zwan, Cees Gooijer, Jan N. M. Commandeur, Nico P. E. Vermeulen, Chris Oostenbrink

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 547 KB

english, 2008

24

Molecular mechanism of allosteric communication in the human PPARα-RXRα heterodimer

Tuomas Venäläinen, Ferdinand Molnár, Chris Oostenbrink, Carsten Carlberg, Mikael Peräkylä

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2010

Language:

english

File:

PDF, 757 KB

english, 2010

25

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

Indira Chandrasekhar, Mika Kastenholz, Roberto D. Lins, Chris Oostenbrink, Lukas D. Schuler, D. Peter Tieleman, Wilfred F. van Gunsteren

Journal:

European Biophysics Journal

Year:

2003

Language:

english

File:

PDF, 388 KB

english, 2003

26

Validation of the 53A6 GROMOS force field

Chris Oostenbrink, Thereza A. Soares, Nico F. A. van der Vegt, Wilfred F. van Gunsteren

Journal:

European Biophysics Journal

Year:

2005

Language:

english

File:

PDF, 530 KB

english, 2005

27

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

Chris de Graaf, Chris Oostenbrink, Peter H. J. Keizers, Barbara M. A. van Vugt-Lussenburg, Jan N. M. Commandeur, Nico P. E. Vermeulen

Journal:

European Biophysics Journal

Year:

2007

Language:

english

File:

PDF, 447 KB

english, 2007

28

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

Jozef Hritz, Tilman Läppchen, Chris Oostenbrink

Journal:

European Biophysics Journal

Year:

2010

Language:

english

File:

PDF, 355 KB

english, 2010

29

On using oscillating time-dependent restraints in MD simulation

Bettina Keller, Markus Christen, Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Journal of Biomolecular NMR

Year:

2007

Language:

english

File:

PDF, 533 KB

english, 2007

30

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

Bren, Urban, Oostenbrink, Chris

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 5.72 MB

english, 2012

31

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

Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Chemistry - A European Journal

Year:

2005

Language:

english

File:

PDF, 318 KB

english, 2005

32

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

Malde, Alpeshkumar K., Zuo, Le, Breeze, Matthew, Stroet, Martin, Poger, David, Nair, Pramod C., Oostenbrink, Chris, Mark, Alan E.

Journal:

Journal of Chemical Theory and Computation

Year:

2011

Language:

english

File:

PDF, 1.76 MB

english, 2011

33

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

de Beer, Stephanie B.A., Venkataraman, Harini, Geerke, Daan P., Oostenbrink, Chris, Vermeulen, Nico P.E.

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.72 MB

english, 2012

34

Efficient Free Energy Calculations for Compounds with Multiple Stable Conformations Separated by High Energy Barriers

Hritz, Jozef, Oostenbrink, Chris

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.57 MB

english, 2009

35

Virtual Screening and Prediction of Site of Metabolism for Cytochrome P450 1A2 Ligands

Vasanthanathan, Poongavanam, Hritz, Jozef, Taboureau, Olivier, Olsen, Lars, Steen Jørgensen, Flemming, Vermeulen, Nico P. E., Oostenbrink, Chris

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 1.68 MB

english, 2009

36

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

Lastdrager, Jeroen, Oostenbrink, Chris, Vasanthanathan, Poongavanam, Commandeur, Jan N. M., Vermeulen, Nico P. E., Jørgensen, Flemming S., Olsen, Lars

Journal:

Year:

2011

Language:

english

File:

PDF, 517 KB

english, 2011

37

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

Denise Steiner, Chris Oostenbrink, Wilfred F. van Gunsteren

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 1.37 MB

english, 2012

38

Molecular dynamics simulations

Tomas Hansson, Chris Oostenbrink, WilfredF van Gunsteren

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 67 KB

english, 2002

39

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

Nagy, Gabor, Oostenbrink, Chris

Journal:

European Biophysics Journal

Year:

2012

Language:

english

File:

PDF, 733 KB

english, 2012

40

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

Ruth Gößler-Schöfberger, Günter Hesser, Maria M. Reif, Jacqueline Friedmann, Bernadette Duscher, José Luis Toca-Herrera, Chris Oostenbrink, Alexander Jilek

Journal:

Archives of Biochemistry and Biophysics

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

41

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

Eva Stjernschantz, Jelle Reinen, Walter Meinl, Beena J. George, Hansruedi Glatt, Nico P.E. Vermeulen, Chris Oostenbrink

Journal:

Molecular and Cellular Endocrinology

Year:

2010

Language:

english

File:

PDF, 1.27 MB

english, 2010

42

Lipid a from lipopolysaccharide recognition: Structure, dynamics and cooperativity by molecular dynamics simulations

Garate, Jose Antonio, Oostenbrink, Chris

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.84 MB

english, 2013

43

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

de Ruiter, Anita, Oostenbrink, Chris

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 3.93 MB

english, 2013

44

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

de Ruiter, Anita, Boresch, Stefan, Oostenbrink, Chris

Journal:

Journal of Computational Chemistry

Year:

2013

Language:

english

File:

PDF, 749 KB

english, 2013

45

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

Jos H.M. Lange, Jennifer Venhorst, Maria J.P. van Dongen, Jurjen Frankena, Firas Bassissi, Natasja M.W.J. de Bruin, Cathaline den Besten, Stephanie B.A. de Beer, Chris Oostenbrink, Natalia Markova, Ch

Journal:

European Journal of Medicinal Chemistry

Year:

2011

Language:

english

File:

PDF, 725 KB

english, 2011

46

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

Reif, Maria M., Hünenberger, Philippe H., Oostenbrink, Chris

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 701 KB

english, 2012

47

Improved Ligand-Protein Binding Affinity Predictions Using Multiple Binding Modes

Stjernschantz, Eva, Oostenbrink, Chris

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 544 KB

english, 2010

48

Fast and Efficient Calculations of Binding Affinities for C8-Substituted GTP Analogues to the FtsZ Protein

Hritz, Jozef, Läppchen, Tilman, Oostenbrink, Chris

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 50 KB

english, 2011

49

Configurational Entropy Change of Netropsin and Distamycin upon DNA Minor-Groove Binding

Dolenc, Jožica, Baron, Riccardo, Oostenbrink, Chris, Koller, Jože, van Gunsteren, Wilfred F.

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 391 KB

english, 2006

50

An Effective Force Field for Molecular Dynamics Simulations of Dimethyl Sulfoxide and Dimethyl Sulfoxide−Water Mixtures

Geerke, Daan P., Oostenbrink, Chris, van der Vegt, Nico F. A., van Gunsteren, Wilfred F.

Journal:

Journal of Physical Chemistry B

Year:

2004

Language:

english

File:

PDF, 151 KB

english, 2004