Daan P Geerke

Digital author ID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2017-2023
Publications (10 Years): 20

Top Topics

Drug Administration

Molecular Dynamics Simulations

Capillary Electrophoresis

Top Venues

Chemistry (Weinheim an der Bergstrasse, Germany)

Journal of chemical theory and computation

Journal of chemical information and modeling

Journal of computer-aided molecular design

This page only lists publications with an associated author ORCID identifier.

Publications

Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J P Hopstaken, Mirte N Pascha, Cornelis A M de Haan, Daan P Geerke, David A Poole, Seino A K Jongkees
An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry (Weinheim an der Bergstrasse, Germany) 29 (14) (2023)
Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J P Hopstaken, Mirte N Pascha, Cornelis A M de Haan, Daan P Geerke, David A Poole, Seino A K Jongkees
An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry (Weinheim an der Bergstrasse, Germany) 29 (14) (2023)
Martin Stroet, Bertrand Caron, Martin S Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen M Visscher, Josef Holownia, Callum Macfarlane, Brian J Bennion, Svetlana Gelpi-Dominguez, Felice C Lightstone, Tijs van der Storm, Daan P Geerke, Alan E Mark, Gunnar W Klau
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. Journal of computer-aided molecular design (2023)
Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick H N Celie, Daan P Geerke, Robbie P Joosten, Anastassis Perrakis
Distant sequence regions of JBP1 contribute to J-DNA binding. Life science alliance 6 (9) (2023)
Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J P Hopstaken, Mirte N Pascha, Cornelis A M de Haan, Daan P Geerke, David A Poole, Seino A K Jongkees
An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry (Weinheim an der Bergstrasse, Germany) 29 (14) (2023)
Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J P Hopstaken, Mirte N Pascha, Cornelis A M de Haan, Daan P Geerke, David A Poole, Seino A K Jongkees
An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation. Chemistry (Weinheim an der Bergstrasse, Germany) (2022)
Thomas Hansen, Xiaobo Sun, Marco Dalla Tiezza, Willem-Jan van Zeist, Joost N P van Stralen, Daan P Geerke, Lando P Wolters, Jordi Poater, Trevor A Hamlin, Friedrich Matthias Bickelhaupt
C-X Bond Activation by Palladium: Steric Shielding versus Steric Attraction. Chemistry (Weinheim an der Bergstrasse, Germany) 28 (44) (2022)
Eko Aditya Rifai, Valerio Ferrario, Juergen Pleiss, Daan P Geerke
Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation. Journal of chemical theory and computation 16 (2) (2020)
Koen M Visscher, Daan P Geerke
Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration. The journal of physical chemistry. B 124 (9) (2020)
Rosa A Luirink, Marlies C A Verkade-Vreeker, Jan N M Commandeur, Daan P Geerke
A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion. Chembiochem : a European journal of chemical biology 21 (10) (2020)
Nele Van Der Steen, Karen Zwaenepoel, Giulia Mazzaschi, Rosa A Luirink, Daan P Geerke, Ken Op de Beeck, Christophe Hermans, Marcello Tiseo, Paul Van Schil, Filip Lardon, Paul Germonpré, Christian Rolfo, Elisa Giovannetti, Godefridus J Peters, Patrick Pauwels
The Role of c-Met as a Biomarker and Player in Innate and Acquired Resistance in Non-Small-Cell Lung Cancer: Two New Mutations Warrant Further Studies. Molecules (Basel, Switzerland) 24 (24) (2019)
Koen M Visscher, Daan P Geerke
Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model. Journal of chemical theory and computation 15 (3) (2019)
Karla Frydenvang, Marlies C A Verkade-Vreeker, Floor Dohmen, Jan N M Commandeur, Maria Rafiq, Osman Mirza, Flemming Steen Jørgensen, Daan P Geerke
Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol. PloS one 14 (5) (2019)
Eko Aditya Rifai, Marc van Dijk, Nico P E Vermeulen, Arry Yanuar, Daan P Geerke
A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation. Journal of chemical information and modeling 59 (9) (2019)
Koen M Visscher, William C Swope, Daan P Geerke
A QM/MM Derived Polarizable Water Model for Molecular Simulation. Molecules (Basel, Switzerland) 23 (12) (2018)
Martin Stroet, Bertrand Caron, Koen M Visscher, Daan P Geerke, Alpeshkumar K Malde, Alan E Mark
Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane. Journal of chemical theory and computation 14 (11) (2018)
Luigi Capoferri, Marc van Dijk, Ariën S Rustenburg, Tsjerk A Wassenaar, Derk P Kooi, Eko Aditya Rifai, Nico P E Vermeulen, Daan P Geerke
eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations. Journal of cheminformatics 9 (1) (2017)
Eko Aditya Rifai, Marc van Dijk, Nico P E Vermeulen, Daan P Geerke
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. Journal of computer-aided molecular design 32 (1) (2017)
Daniël Verhoef, Koen M Visscher, C Ruben Vosmeer, Ka Lei Cheung, Pieter H Reitsma, Daan P Geerke, Mettine H A Bos
Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors. Nature communications 8 (1) (2017)
Marc van Dijk, Antonius M Ter Laak, Jörg D Wichard, Luigi Capoferri, Nico P E Vermeulen, Daan P Geerke
Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors. Journal of chemical information and modeling 57 (9) (2017)