Deriving Force-Field Parameters from First Principles Using a Polarizable and Higher Order Dispersion Model

por Visscher, Koen M., Geerke, Daan P.
Publicado 2019

Deriving a Polarizable Force Field for Biomolecular Building Blocks with Minimal Empirical Calibration

por Visscher, Koen M., Geerke, Daan P.
Publicado 2020

A QM/MM Derived Polarizable Water Model for Molecular Simulation

por Visscher, Koen M., Swope, William C., Geerke, Daan P.
Publicado 2018

Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations

por Rifai, Eko Aditya, van Dijk, Marc, Geerke, Daan P.
Publicado 2020

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

por Perić-Hassler, Lovorka, Stjernschantz, Eva, Oostenbrink, Chris, Geerke, Daan P.
Publicado 2013

Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation

por Rifai, Eko Aditya, Ferrario, Valerio, Pleiss, Jürgen, Geerke, Daan P.
Publicado 2020

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 Ch...

por Rifai, Eko Aditya, van Dijk, Marc, Vermeulen, Nico P. E., Geerke, Daan P.
Publicado 2017

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach

por Engler, Martin S., Caron, Bertrand, Veen, Lourens, Geerke, Daan P., Mark, Alan E., Klau, Gunnar W.
Publicado 2019

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1–Ligand Binding Free Energy Calculation

por Rifai, Eko Aditya, van Dijk, Marc, Vermeulen, Nico P. E., Yanuar, Arry, Geerke, Daan P.
Publicado 2019

A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450‐Catalyzed Substrate Conversion

por Luirink, Rosa A., Verkade‐Vreeker, Marlies C. A., Commandeur, Jan N. M., Geerke, Daan P.
Publicado 2020

Distant sequence regions of JBP1 contribute to J-DNA binding

por de Vries, Ida, Ammerlaan, Danique, Heidebrecht, Tatjana, Celie, Patrick HN, Geerke, Daan P, Joosten, Robbie P, Perrakis, Anastassis
Publicado 2023

Improving the iterative Linear Interaction Energy approach using automated recognition of configurational transitions

por Vosmeer, C. Ruben, Kooi, Derk P., Capoferri, Luigi, Terpstra, Margreet M., Vermeulen, Nico P. E., Geerke, Daan. P.
Publicado 2016

Towards Automated Binding Affinity Prediction Using an Iterative Linear Interaction Energy Approach

por Vosmeer, C. Ruben, Pool, René, van Stee, Mariël F., Perić-Hassler, Lovorka, Vermeulen, Nico P. E., Geerke, Daan P.
Publicado 2014

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

por van Dijk, Marc, ter Laak, Antonius M., Wichard, Jörg D., Capoferri, Luigi, Vermeulen, Nico P. E., Geerke, Daan P.
Publicado 2017

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

por Verhoef, Daniël, Visscher, Koen M., Vosmeer, C. Ruben, Cheung, Ka Lei, Reitsma, Pieter H., Geerke, Daan P., Bos, Mettine H. A.
Publicado 2017

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

por Capoferri, Luigi, Verkade-Vreeker, Marlies C. A., Buitenhuis, Danny, Commandeur, Jan N. M., Pastor, Manuel, Vermeulen, Nico P. E., Geerke, Daan P.
Publicado 2015

An anti-tuberculosis compound screen using a zebrafish infection model identifies an aspartyl-tRNA synthetase inhibitor

por Habjan, Eva, Ho, Vien Q. T., Gallant, James, van Stempvoort, Gunny, Jim, Kin Ki, Kuijl, Coen, Geerke, Daan P., Bitter, Wilbert, Speer, Alexander
Publicado 2021

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

por Capoferri, Luigi, van Dijk, Marc, Rustenburg, Ariën S., Wassenaar, Tsjerk A., Kooi, Derk P., Rifai, Eko A., Vermeulen, Nico P. E., Geerke, Daan P.
Publicado 2017

Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol

por Frydenvang, Karla, Verkade-Vreeker, Marlies C. A., Dohmen, Floor, Commandeur, Jan N. M., Rafiq, Maria, Mirza, Osman, Jørgensen, Flemming Steen, Geerke, Daan P.
Publicado 2019

C−X Bond Activation by Palladium: Steric Shielding versus Steric Attraction

por Hansen, Thomas, Sun, Xiaobo, Dalla Tiezza, Marco, van Zeist, Willem‐Jan, van Stralen, Joost N. P., Geerke, Daan P., Wolters, Lando P., Poater, Jordi, Hamlin, Trevor A., Bickelhaupt, F. Matthias
Publicado 2022