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Research Output 2003 2018

  • 48 Article
  • 1 PhD Thesis - Research VU, graduation VU
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Article
2018
Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes
2017
Open Access
Free energy
free energy
Ligands
Drug Design
Molecular Dynamics Simulation
Open Access
Aromatase Inhibitors
Cytochrome P-450 Enzyme System
energy
interaction
workflow

Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors

Verhoef, D., Visscher, K. M., Vosmeer, C. R., Cheung, K. L., Reitsma, P. H., Geerke, D. P. & Bos, M. H. A. 13 Sep 2017 In : Nature Communications. 8, 1, p. 528

Research output: Contribution to journalArticle

Open Access
Factor Xa
inhibitors
Coagulation
Blood Coagulation Factor Inhibitors
Anticoagulants
Open Access

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations

Capoferri, C. L., van Dijk, M., Rustenburg, A. S., Wassenaar, T., Kooi, D. P., Rifai, E. A., Vermeulen, N. P. E. & Geerke, D. P. 2017 In : Journal of Cheminformatics. 9, 58, p. 1-13 13 p.

Research output: Contribution to journalArticle

Open Access
Pipelines
Ligands
energy
ligands
Free energy
2016

Combined simulation and mutation studies to elucidate selectivity of unsubstituted amphetamine-like cathinones at the dopamine transporter.

Seddik, A., Geerke, D. P., Stockner, T., Holy, M., Kudlacek, O., Cozzi, N. V., Ruoho, A. E., Sitte, H. H. & Ecker, G. F. 2016 (Accepted/In press) In : Molecular Informatics.

Research output: Contribution to journalArticle

Open Access

Insights into regioselective metabolism of mefenamic acid by cytochrome P450 BM3 mutants through crystallography, docking, molecular dynamics, and free energy calculations.

Capoferri, L., Leth, R., ter Haar, E., Mohanty, A. K., Grootenhuis, P. D. J., Vottero, E. R., Commandeur, J. N. M., Vermeulen, N. P. E., Jorgensen, F. S., Olsen, L. & Geerke, D. P. 2016 In : Proteins. 84, 3, p. 383-396

Research output: Contribution to journalArticle

To Polarize or not to Polarize? Charge-on-Spring versus KBFF models for water and methanol bulk and vapor-liquid interfacial mixtures.

Ploetz, E. A., Rustenburg, A. S., Geerke, D. P. & Smith, P. E. 2016 In : Journal of Chemical Theory and Computation. 12, 5, p. 2373-2387

Research output: Contribution to journalArticle

2015

Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project

Sanz, F., Carrio, P., Lopez, O., Capoferri, L., Kooi, D. P., Vermeulen, N. P. E., Geerke, D. P., Montanari, F., Ecker, G. F., Schwab, C. H., Kleinoeder, T., Magdziarz, T. & Pastor, M. Jun 2015 In : Molecular Informatics. 34, 6-7, p. 477-484

Research output: Contribution to journalArticle

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation

Capoferri, L., Verkade-Vreeker, M. C. A., Buitenhuis, D., Commandeur, J. N. M., Pastor, M., Vermeulen, N. P. E. & Geerke, D. P. 9 Nov 2015 In : PLoS One. 10, 11

Research output: Contribution to journalArticle

Open Access
2014

A Comparison Between QM/MM And QM/QM Based Fitting of Condensed-Phase Atomic Polarizabilities

Vosmeer, C. R., Kiewisch, K., Keijzer, K., Visscher, L. & Geerke, D. P. 2014 In : Physical Chemistry Chemical Physics - PCCP. 16, p. 17857-17862

Research output: Contribution to journalArticle

Molecules
Dipole moment
Methanol
Electric fields
Polarization

Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs

Venkataraman, H., Verkade-Vreeker, M. C. A., Capoferri, L., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M. 15 Oct 2014 In : Bioorganic and Medicinal Chemistry. 22, 20, p. 5613-5620

Research output: Contribution to journalArticle

Genetics and evolution of anthocyanin methylation.

Provenzano, S., Spelt, C. E., Hosokawa, S., Nakamura, N., Brugliera, F., Demelis, L., Geerke, D. P., Schubert, A., Tanaka, Y., Quattrocchio, F. M. & Koes, R. E. 2014 In : Plant Physiology. 165, p. 962-977

Research output: Contribution to journalArticle

Molecular Evolution
Anthocyanins
methylation
Methylation
anthocyanins

Mutation in KERA Identified by Linkage Analysis and Targeted Resequencing in a Pedigree with Premature Atherosclerosis

Maiwald, S. , Sivapalaratnam, S. , Motazacker, M. M. , van Capelleveen, J. C. , Bot, I. , de Jager, S. C. , van Eck, M. , Jolley, J. , Kuiper, J. , Stephens, J. , Albers, C. A. , Vosmeer, C. R. , Kruize, H. , Geerke, D. P. , van der Wal, A. C. , van der Loos, C. M. , Kastelein, J. J. P. , Trip, M. D. , Ouwehand, W. H. , Dallinga-Thie, G. M. & 1 others Hovingh, G. K. 30 May 2014 In : PLoS One. 9, 5

Research output: Contribution to journalArticle

Open Access

Towards automated binding affinity prediction using an iterative linear interaction energy approach

Vosmeer, C. R., Pool, R., van Stee, M. F., Peric-Hassler, L., Vermeulen, N. P. E. & Geerke, D. P. 2014 In : International Journal of Molecular Sciences. 15, 1, p. 798-816 19 p.

Research output: Contribution to journalArticle

Open Access
affinity
Ligands
proteins
Proteins
Protein Conformation
2013

Charge group partitioning in biomolecular simulation

Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K., Malde, A. K., Mark, A. E., Geerke, D. P., Stougie, L. & Klau, G. W. 2013 In : Journal of Computational Biology. 20, 3, p. 188-198

Research output: Contribution to journalArticle

Hardness
Partitioning
Charge
Force Field
Molecules

CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

Peric-Hassler, L., Stjernschantz, E. M., Oostenbrink, B. C. & Geerke, D. P. 2013 In : International Journal of Molecular Sciences. 14, 12, p. 24514-24530

Research output: Contribution to journalArticle

Open Access
Cytochrome P-450 CYP2D6
Protein Conformation
affinity
Conformations
Ligands
2012

A single active site mutation inverts stereoselectivity of 16-hydroxylation of testosterone catalyzed by engineered cytochrome P450 BM3.

Venkataraman, H., de Beer, S. B., Bergen, L. A., van Essen, N., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M. 2012 In : ChemBioChem. 13, 4, p. 520-523

Research output: Contribution to journalArticle

Charge Group Partitioning in Biomolecular Simulation

Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K. M., Malde, A. K., Mark, A. E., Geerke, D. P., Stougie, L. & Klau, G. W. 2012 In : Lecture Notes in Computer Science. 7262, p. 29-43

Research output: Contribution to journalArticle

Hydroxylation
Cytochrome P-450 Enzyme System
Free energy
energy
Substrates

Impaired bortezomib binding to mutant beta 5 subunit of the proteasome is the underlying basis for bortezomib resistance in leukemia cells.

Franke, N. E., Niewerth, D., Assaraf, Y. G., van Meerloo, J., Vojtekova, K., van Zantwijk, C. H., Zweegman, S., Chan, E. T., Geerke, D. P., Schimmer, A. D., Kaspers, G. J. L., Jansen, G. & Cloos, J. 2012 In : Leukemia. 26, 4, p. 757-768

Research output: Contribution to journalArticle

Proteasome Endopeptidase Complex
Leukemia
Mutation
Proteasome Inhibitors
Drug Resistance

New functionalities in the GROMOS biomolecular simulation software

Kunz, A. P. E., Allison, J. R., Geerke, D. P., Horta, B. A. C., Hünenberger, P. H., Riniker, S., Schmid, N. & van Gunsteren, W. F. 2012 In : Journal of Computational Chemistry. 33, 3, p. 340-353 13 p.

Research output: Contribution to journalArticle

Simulation Software
Molecular dynamics
Switching functions
Solvation
Implicit Surfaces

QM/MM based fitting of atomic polarizabilities for use in condensed-phase biomolecular simulation

Vosmeer, C. R., Rustenburg, A. S., Rice, J. E., Horn, H. W., Swope, W. C. & Geerke, D. P. 2012 In : Journal of Chemical Theory and Computation. 8, 10, p. 3839-3853

Research output: Contribution to journalArticle

Gases
Polarization
field theory (physics)
simulation
vapor phases
Hydroxylation
Enantiomers
Cytochrome P-450 Enzyme System
Stereoselectivity
Biocatalysts
Regioselectivity
Hydroxylation
Cytochrome P-450 Enzyme System
Plasticity
Testosterone
2011

GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

Eichenberger, A. P., Allison, J. R., Dolenc, J., Geerke, D. P., Horta, B. A. C., Meier, K., Oostenbrink, B. C., Schmid, N., Steiner, D., Wang, D. & van Gunsteren, W. F. 2011 In : Journal of Chemical Theory and Computation. 7, p. 3379-3390 13 p.

Research output: Contribution to journalArticle

Trajectories
trajectories
computer programs
simulation
Structural dynamics

Insights into the binding mode of propafenone type P-glycoprotein inhibitors

Klepsch, F., Vosmeer, C. R., Geerke, D. P., Oostenbrink, C. & Ecker, G. F. 27 Mar 2011 In : Abstracts of Papers - American Chemical Society. 241

Research output: Contribution to journalArticle

2010
2009

On the direct calculation of the free energy of quantization for molecular systems in the condensed phase

Geerke, D. P., Luber, S., Marti, K. H. & Van Gunsteren, W. F. 2009 In : Journal of Computational Chemistry. 30, 4, p. 514-23

Research output: Contribution to journalArticle

QM-MM interactions in simulations of liquid water using combined semi-empirical/classical Hamiltonians

Geerke, D. P., Thiel, S., Thiel, W. & van Gunsteren, W. F. 2008 In : Physical Chemistry Chemical Physics - PCCP. 10, 2, p. 297-302

Research output: Contribution to journalArticle

2007
2006

Biomolecular modeling: Goals, problems, perspectives

van Gunsteren, W. F., Bakowies, D., Baron, R., Chandrasekhar, I., Christen, M., Daura, X., Gee, P., Geerke, D. P., Glattli, A., Hunenberger, P. H., Kastenholz, M., Oostenbrink, C., Schenk, M., Trzesniak, D., van der Vegt, N. F. A. & Yu, H. B. 2006 In : Angewandte Chemie International Edition in English. 45, 25, p. 4064-92

Research output: Contribution to journalArticle

Biophysics
Sampling
Time series
Computer simulation
Experiments

Force field evaluation for biomolecular simulation: Free enthalpies of solvation of polar and apolar compounds in various solvents

Geerke, D. P. & van Gunsteren, W. F. 13 Mar 2006 In : Chemphyschem. 7, 3, p. 671-678

Research output: Contribution to journalArticle

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models

Yu, H., Geerke, D. P., Liu, H. & van Gunsteren, W. E. Oct 2006 In : Journal of Computational Chemistry. 27, 13, p. 1494-1504

Research output: Contribution to journalArticle

2005

DFT benchmark study for the oxidative addition of CH4 to Pd. Performance of various density functionals

de Jong, G. T., Geerke, D. P., Diefenbach, A. & Bickelhaupt, F. M. 2005 In : Chemical Physics. 313, 1-3, p. 261-270

Research output: Contribution to journalArticle

functionals
Density functional theory
density functional theory
approximation
Potential energy surfaces

Oxidative addition of the ethane C-C bond to Pd. An ab initio benchmark and DFT validation study

De Jong, G. T., Geerke, D. P., Diefenbach, A., Sola, M. & Bickelhaupt, F. M. 2005 In : Journal of Computational Chemistry. 26, 10, p. 1006-20

Research output: Contribution to journalArticle

Potential energy surfaces
Ethane
Palladium
Discrete Fourier transforms
Potential Energy Surface

The GROMOS software for biomolecular simulation: GROMOS05

Christen, M., Hunenberger, P. H., Bakowies, D., Baron, R., Burgi, R., Geerke, D. P., Heinz, T. N., Kastenholz, M., Krautler, V., Oostenbrink, C., Peter, C., Trzesniak, D. & van Gunsteren, W. F. 2005 In : Journal of Computational Chemistry. 26, 16, p. 1719-51

Research output: Contribution to journalArticle

Molecular dynamics
Molecular Simulation
Molecules
Biomolecules
Software
2004

An effective force field for molecular dynamics simulations of dimethyl sulfoxide and dimethyl sulfoxide-water mixtures

Geerke, D. P., Oostenbrink, C., van der Vegt, N. F. A. & van Gunsteren, W. F. 2004 In : Journal of Physical Chemistry B. 108, 4, p. 1436-1445

Research output: Contribution to journalArticle

On the transferability of the SPCAL water model to biomolecular simulation

Glattli, A., Oostenbrink, C., Daura, X., Geerke, D. P., Yu, H. B. & van Gunsteren, W. F. 2004 In : Brazilian Journal of Physics. 34, 1, p. 116-125

Research output: Contribution to journalArticle

Open Access
File

Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method

van Lipzig, M. M. H., ter Laak, A. M., Jongejan, A., Vermeulen, N. P. E., Wamelink, M. M., Geerke, D. P. & Meerman, J. H. N. 2004 In : Journal of Medicinal Chemistry. 47, 4, p. 1018-30

Research output: Contribution to journalArticle

Molecular Dynamics Simulation
Estrogen Receptors
Ligands
Estrogens
Diethylstilbestrol
2003

Molecular dynamics simulations with the estrogen receptor: Prediction of ligand binding affinity and orientation by the linear interaction energy method

van Lipzig, M. M. H., Vermeulen, N. P. E., Wamelink, M. M., Geerke, D., Jongejan, A., ter Laak, T. M. & Meerman, J. H. N. 2003 In : Drug Metabolism Reviews. 35, p. 107-107

Research output: Contribution to journalArticle