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List of works by Marc van der Kamp

A Multiscale Simulation Approach to Modeling Drug-Protein Binding Kinetics

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase.

scientific article

Ab initio QM/MM modelling of acetyl-CoA deprotonation in the enzyme citrate synthase

scientific article published on 08 April 2007

Affinity of Avr2 for tomato cysteine protease Rcr3 correlates with the Avr2-triggered Cf-2-mediated hypersensitive response

scientific article published in January 2011

An Efficient Computational Assay for β-Lactam Antibiotic Breakdown by Class A β-Lactamases

scientific article published on 07 August 2019

An Esterase-like Lyase Catalyzes Acetate Elimination in Spirotetronate/Spirotetramate Biosynthesis

scientific article published on 21 January 2019

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

scientific article published on 21 April 2017

Biomolecular simulation and modelling: status, progress and prospects

scientific article published on December 2008

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

scientific article published on 12 April 2013

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

scientific article published on April 2014

Comparison of different quantum mechanical/molecular mechanics boundary treatments in the reaction of the hepatitis C virus NS3 protease with the NS5A/5B substrate

scientific article published on 13 October 2007

Computational enzymology: insight into biological catalysts from modelling

scientific article published on 06 August 2008

Conformational change and ligand binding in the aristolochene synthase catalytic cycle

scientific article

Crystal structure of the putative cyclase IdmH from the indanomycin nonribosomal peptide synthase/polyketide synthase

scientific article published on 24 October 2019

Diverse effects on the native β-sheet of the human prion protein due to disease-associated mutations

scientific article

Dynameomics: a comprehensive database of protein dynamics

scientific article

Dynameomics: protein dynamics and unfolding across fold space

scientific article published in December 2010

Dynamical origins of heat capacity changes in enzyme-catalysed reactions

scientific article published on 21 March 2018

Enzymatic synthesis of natural (+)-aristolochene from a non-natural substrate.

scientific article published on 17 November 2016

Experiment and Simulation Reveal How Mutations in Functional Plasticity Regions Guide Plant Monoterpene Synthase Product Outcome

article

Exposing the Interplay Between Enzyme Turnover, Protein Dynamics, and the Membrane Environment in Monoamine Oxidase B

scientific article published on 23 April 2019

High-level QM/MM modelling predicts an arginine as the acid in the condensation reaction catalysed by citrate synthase

scientific article published on 11 March 2008

How Static Disorder Mimics Decoherence in Anisotropy Pump-Probe Experiments on Purple-Bacteria Light Harvesting Complexes

scientific article

Identification of the quinolinedione inhibitor binding site in Cdc25 phosphatase B through docking and molecular dynamics simulations

scientific article published on 9 October 2017

Influence of pH on the human prion protein: insights into the early steps of misfolding

scientific article

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations

scientific article published on January 2011

Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins

scientific article published on 05 August 2020

Multiscale Simulations of Clavulanate Inhibition Identify the Reactive Complex in Class A β-Lactamases and Predict the Efficiency of Inhibition

scientific article published on 07 June 2018

Multiscale analysis of enantioselectivity in enzyme-catalysed 'lethal synthesis' using projector-based embedding

scientific article published on 14 February 2018

On the Temperature Dependence of Enzyme-Catalyzed Rates.

scientific article published on 8 March 2016

Pathogenic mutations in the hydrophobic core of the human prion protein can promote structural instability and misfolding

scientific article

Peptide cargo tunes a network of correlated motions in human leucocyte antigens

scientific article published on 05 March 2020

QM/MM modelling of ketosteroid isomerase reactivity indicates that active site closure is integral to catalysis

scientific article published on 27 February 2013

QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

scientific article published on December 2014

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes

scientific article published on 01 June 2018

Quantum Mechanics/Molecular Mechanics Simulations Identify the Ring-Opening Mechanism of Creatininase

scientific article published on 15 November 2017

Rapid Estimation of Catalytic Efficiency by Cumulative Atomic Multipole Moments: Application to Ketosteroid Isomerase Mutants.

scientific article published on 19 January 2017

Reaction Mechanism of N -Acetylneuraminic Acid Lyase Revealed by a Combination of Crystallography, QM/MM Simulation, and Mutagenesis ⬇️

scientific article

Reliable <i>In Silico</i> Ranking of Engineered Therapeutic TCR Binding Affinities with MMPB/GBSA

scientific article published on 20 January 2022

Simulations of membrane-bound diglycosylated human prion protein reveal potential protective mechanisms against misfolding

scientific article published on 13 April 2017

Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.

scientific article published on 9 August 2017

Structural and dynamic properties of the human prion protein

scientific article

Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions.

scientific article

Substrate polarization in enzyme catalysis: QM/MM analysis of the effect of oxaloacetate polarization on acetyl-CoA enolization in citrate synthase

article

Taming the Reactivity of Monoterpene Synthases To Guide Regioselective Product Hydroxylation

scientific article published on 03 December 2019

Testing high-level QM/MM methods for modeling enzyme reactions: acetyl-CoA deprotonation in citrate synthase

scientific article published on September 2010

The Catalytic Mechanism of a Natural Diels-Alderase Revealed in Molecular Detail ⬇️

scientific article

The basis for carbapenem hydrolysis by class A β-lactamases: a combined investigation using crystallography and simulations

scientific article

The consequences of pathogenic mutations to the human prion protein

scientific article published on 14 July 2009

The predominance of nucleotidyl activation in bacterial phosphonate biosynthesis

scientific article published on 16 August 2019

Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site

scientific article published on 15 April 2019

Visualizing the protons in a metalloenzyme electron proton transfer pathway

scientific article published on 09 March 2020

“Lethal Synthesis” of Fluorocitrate by Citrate Synthase Explained through QM/MM Modeling

scientific article published on 16 September 2011

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