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Research Output 2003 2018

  • 48 Article
  • 1 Conference contribution
  • 1 PhD Thesis - Research VU, graduation VU
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Article
2018

A combined computational and experimental study on selective flucloxacillin hydroxylation by cytochrome P450 BM3 variants

Luirink, R. A., Dekker, S. J., Capoferri, L., Kuiper, C. L., Janssen, L. F. H., Ari, M. E., Vermeulen, N. P. E., Vos, J. C., Commandeur, J. N. M. & Geerke, D. P., Jul 2018, In : Journal of Inorganic Biochemistry. 184, p. 115-122 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes
2017

A Systematic Approach to Calibrate a Transferable Polarizable Force Field Parameter Set for Primary Alcohols

Visscher, K. M., Vosmeer, C. R., Luirink, R. A. & Geerke, D. P., Mar 2017, In : Journal of Computational Chemistry. 38, 8, p. 508-517

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Free energy
free energy
Ligands
Drug Design
Molecular Dynamics Simulation

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors

van Dijk, M., Ter Laak, A. M., Wichard, J. D., Capoferri, L., Vermeulen, N. P. E. & Geerke, D. P., 25 Sep 2017, In : Journal of Chemical Information and Modeling. 57, 9, p. 2294-2308 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Improving the iterative linear interaction energy approach using automated recognition of configurational transitions.

Vosmeer, C. R., Kooi, D. P., Capoferri, L., Terpstra, M. M., Vermeulen, N. P. E. & Geerke, D. P., 2016, In : Journal of Molecular Modeling. 1, 31

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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, SB., Bergen, LA., 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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Free energy calculations give insight into the stereoselective hydroxylation of α-ionones by engineered cytochrome P450 BM3 mutants

De Beer, S. B., Venkataraman, H., Geerke, D. P., Oostenbrink, C. & Vermeulen, N. P. E., 2012, In : Journal of Chemical Information and Modeling. 52, 8, p. 2139-2148

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

Gases
Polarization
field theory (physics)
simulation
vapor phases

Regio- and Stereoselective Hydroxylation of Optically Active α-Ionone Enantiomers by Engineered Cytochrome P450 BM3 Mutants

Venkataraman, H., de Beer, S. B. A., Geerke, D. P., Vermeulen, N. P. E. & Commandeur, J. N. M., 2012, In : Advanced Synthesis and Catalysis. 354, 11-12, p. 2172-2184

Research output: Contribution to JournalArticleAcademicpeer-review

Hydroxylation
Enantiomers
Cytochrome P-450 Enzyme System
Stereoselectivity
Biocatalysts

The role of protein plasticity in computational rationalization studies on regioselectivity in testosterone hydroxylation by Cytochrome P450 BM3 mutants

de Beer, S. B. A., van Bergen, L. A. H., Keijzer, K., Rea, V., Venkataraman, H., Fonseca Guerra, C., Bickelhaupt, F. M., Vermeulen, N. P. E., Commandeur, J. N. M. & Geerke, D. P., 2012, In : Current Drug Metabolism. 13, 2, p. 155-166

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

2010

Molecular dynamics simulations of the interaction between polyhydroxylated compounds and Lennard-Jones walls: preferential affinity/exclusion effects and their relevance for bioprotection

Geerke, D. P., Van Gunsteren, W. F. & Hünenberger, P. H., 2010, In : Molecular Simulation. 36, 9, p. 708-728 20 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

2008

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 JournalArticleAcademicpeer-review

2007

Calculation of the free energy of polarization: Quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters

Geerke, D. P. & van Gunsteren, W. F., 14 Jun 2007, In : Journal of Physical Chemistry B. 111, 23, p. 6425-6436

Research output: Contribution to JournalArticleAcademicpeer-review

Combined QM/MM molecular dynamics study on a condensed-phase S(N)2 reaction at nitrogen: The effect of explicitly including solvent polarization

Geerke, D. P., Thiel, S., Thiel, W. & van Gunsteren, W. F., 2007, In : Journal of Chemical Theory and Computation. 3, 4, p. 1499-1509

Research output: Contribution to JournalArticleAcademicpeer-review

On the calculation of atomic forces in classical simulation using the charge-on-spring method to explicitly treat electronic polarization

Geerke, D. P. & van Gunsteren, W. F., 2007, In : Journal of Chemical Theory and Computation. 3, 6, p. 2128-2137

Research output: Contribution to JournalArticleAcademicpeer-review

The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures

Geerke, D. P. & van Gunsteren, W. F., 2007, In : Molecular Physics. 105, 13-14, p. 1861-1881

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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, DP. & van Gunsteren, WF., 13 Mar 2006, In : ChemPhysChem. 7, 3, p. 671-678

Research output: Contribution to JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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 JournalArticleAcademicpeer-review

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, MMH., Vermeulen, NPE., Wamelink, M. M., Geerke, D., Jongejan, A., ter Laak, TM. & Meerman, JHN., 2003, In : Drug Metabolism Reviews. 35, p. 107-107

Research output: Contribution to JournalArticleAcademicpeer-review