Search filters

List of works by Daan P Geerke

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

scientific article published on 11 September 2019

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

scientific article published on 09 January 2020

A QM/MM Derived Polarizable Water Model for Molecular Simulation

article published in 2018

A comparison between QM/MM and QM/QM based fitting of condensed-phase atomic polarizabilities

scientific article published on 01 September 2014

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

scientific article

A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

scientific article published on 01 March 2017

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

scientific article

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

scientific article published on 05 February 2019

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.

scientific article published on 9 September 2017

Biomolecular modeling: Goals, problems, perspectives

scientific article published on June 2006

CYP 2D6 binding affinity predictions using multiple ligand and protein conformations

scientific article published on 17 December 2013

Calculation of the Free Energy of Polarization: Quantifying the Effect of Explicitly Treating Electronic Polarization on the Transferability of Force-Field Parameters

scientific article published on 18 May 2007

Charge group partitioning in biomolecular simulation

scientific article published on March 2013

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

scientific article published on 21 January 2020

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

scientific article published on 04 August 2017

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

scientific article published on 14 February 2019

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

scientific article published on 19 February 2020

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

scientific article published on 13 September 2017

Engineering a self-sufficient Mycobacterium tuberculosis CYP130 by gene fusion with the reductase-domain of CYP102A1 from Bacillus megaterium.

scientific article published on 7 December 2017

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

scientific article published in March 2006

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants

scientific article published on 19 July 2012

GROMOS++ Software for the Analysis of Biomolecular Simulation Trajectories

scientific article published on 16 September 2011

Genetic Control and Evolution of Anthocyanin Methylation

scientific article published on 15 May 2014

Impaired bortezomib binding to mutant β5 subunit of the proteasome is the underlying basis for bortezomib resistance in leukemia cells.

scientific article published on 23 September 2011

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

scientific article

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

scientific article

Integrative Modeling Strategies for Predicting Drug Toxicities at the eTOX Project

scientific article published on 11 June 2015

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

scientific article

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

article

Mutation in KERA identified by linkage analysis and targeted resequencing in a pedigree with premature atherosclerosis

scientific article

New functionalities in the GROMOS biomolecular simulation software

scientific article published on 11 November 2011

On the Calculation of Atomic Forces in Classical Simulation Using the Charge-on-Spring Method To Explicitly Treat Electronic Polarization

article

Oxidative addition of the ethane CC bond to Pd. Anab initiobenchmark and DFT validation study

article

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

scientific article published in February 2004

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

scientific article published in November 2007

QM/MM-Based Fitting of Atomic Polarizabilities for Use in Condensed-Phase Biomolecular Simulation

scientific article published on 27 April 2012

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

scientific article published on 24 May 2019

The Automated Topology Builder Version 3.0 (ATB3.0): Prediction of Solvation Free Enthalpies in Water and Hexane

scientific article published on 22 October 2018

The GROMOS software for biomolecular simulation: GROMOS05.

scientific article

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

scientific article published on 04 December 2019

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

scientific article

To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures

article

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

scientific article published on 9 January 2014

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

scientific article published on 21 November 2017

Paulina is supported by:

About Paulina

Help