Research Output per year
Research Output 2003 2018
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 Journal › Article › Academic › peer-review
Floxacillin
Hydroxylation
Cytochrome P-450 Enzyme System
Metabolites
Enzymes
Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane
Stroet, M., Caron, B., Visscher, K. M., Geerke, D. P., Malde, A. K. & Mark, A. E., 13 Nov 2018, In : Journal of Chemical Theory and Computation. 14, 11, p. 5834-5845 12 p.Research output: Contribution to Journal › Article › Academic › peer-review
Solvation
Hexanes
Hexane
solvation
Enthalpy
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. 508-517Research output: Contribution to Journal › Article › Academic › peer-review
Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2
Rifai, E. A., van Dijk, M., Vermeulen, N. P. E. & Geerke, D. P., 2017, In : Journal of Computer-aided Molecular Design. 11 p.Research output: Contribution to Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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. 528Research output: Contribution to Journal › Article › Academic › peer-review
Open Access
Factor Xa
inhibitors
Coagulation
Blood Coagulation Factor Inhibitors
Anticoagulants
Engineering a self-sufficient Mycobacterium tuberculosis CYP130 by gene fusion with the reductase-domain of CYP102A1 from Bacillus megaterium
Ortega Ugalde, S., Luirink, R. A., Geerke, D. P., Vermeulen, N. P. E., Bitter, W. & Commandeur, J. N. M., 7 Dec 2017, In : Journal of Inorganic Biochemistry. p. 48 53 p., 180Research output: Contribution to Journal › Article › Academic › peer-review
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 Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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, 31Research output: Contribution to Journal › Article › Academic › peer-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. 383-396Research output: Contribution to Journal › Article › Academic › peer-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. 2373-2387Research output: Contribution to Journal › Article › Academic › peer-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. 477-484Research output: Contribution to Journal › Article › Academic › peer-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, 11Research output: Contribution to Journal › Article › Academic › peer-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. 17857-17862Research output: Contribution to Journal › Article › Academic › peer-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. 5613-5620Research output: Contribution to Journal › Article › Academic › peer-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. 962-977Research output: Contribution to Journal › Article › Academic › peer-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 , 30 May 2014, In : PLoS ONE. 9, 5Research output: Contribution to Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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. 188-198Research output: Contribution to Journal › Article › Academic › peer-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. 24514-24530Research output: Contribution to Journal › Article › Academic › peer-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. 520-523Research output: Contribution to Journal › Article › Academic › peer-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. 29-43Research output: Contribution to Journal › Article › Academic › peer-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. 2139-2148Research output: Contribution to Journal › Article › Academic › peer-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. 757-768Research output: Contribution to Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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. 3839-3853Research output: Contribution to Journal › Article › Academic › peer-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. 2172-2184Research output: Contribution to Journal › Article › Academic › peer-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. 155-166Research output: Contribution to Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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. 241Research output: Contribution to Journal › Article › Academic › peer-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 Journal › Article › Academic › peer-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. 514-23Research output: Contribution to Journal › Article › Academic › peer-review
2008
ORGN 211-The effect of steric bulk on Pd, PdCl- and Pd(PH3)(2) catalyzed C-C bond activation: Perspectives from an extended activation strain model
van Zeist, W-J., van Stralen, J. N. P., Geerke, D. P. & Bickelhaupt, F. M., 6 Apr 2008, In : Abstracts of Papers - American Chemical Society. 235Research output: Contribution to Journal › Article › Academic › peer-review
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. 297-302Research output: Contribution to Journal › Article › Academic › peer-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. 6425-6436Research output: Contribution to Journal › Article › Academic › peer-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. 1499-1509Research output: Contribution to Journal › Article › Academic › peer-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. 2128-2137Research output: Contribution to Journal › Article › Academic › peer-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. 1861-1881Research output: Contribution to Journal › Article › Academic › peer-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. 4064-92Research output: Contribution to Journal › Article › Academic › peer-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. 671-678Research output: Contribution to Journal › Article › Academic › peer-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. 1494-1504Research output: Contribution to Journal › Article › Academic › peer-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. 261-270Research output: Contribution to Journal › Article › Academic › peer-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. 1006-20Research output: Contribution to Journal › Article › Academic › peer-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. 1719-51Research output: Contribution to Journal › Article › Academic › peer-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. 1436-1445Research output: Contribution to Journal › Article › Academic › peer-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. 116-125Research output: Contribution to Journal › Article › Academic › peer-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. 1018-30Research output: Contribution to Journal › Article › Academic › peer-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. 107-107Research output: Contribution to Journal › Article › Academic › peer-review