List of works - David van der Spoel

A potential for molecular simulation of compounds with linear moieties

scientific article published on 01 August 2020

A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins

scientific article published in January 2008

A temperature predictor for parallel tempering simulations

scientific article published on 25 February 2008

A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors

scientific article

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

scientific article

Anopheles gambiae, Anoga-HrTH hormone, free and bound structure--a nuclear magnetic resonance experiment

scientific article published on 21 February 2013

Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

scientific article published on 5 January 2016

Atomistic simulation of ion solvation in water explains surface preference of halides.

scientific article published on 11 April 2011

Binding of Pollutants to Biomolecules: A Simulation Study

scientific article published on 7 September 2016

Blind docking of drug-sized compounds to proteins with up to a thousand residues

scientific article published on 31 January 2006

Chemical properties, environmental fate, and degradation of seven classes of pollutants

scientific article published on 28 March 2014

Coherent diffraction of a single virus particle: The impact of a water layer on the available orientational information ⬇️

scientific article published on March 15, 2011

Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents

scientific article

Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations

scientific article published on 14 March 2014

Deciphering solution scattering data with experimentally guided molecular dynamics simulations

scientific article

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

scientific article published on 6 May 2015

Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin

scientific article

Efficient docking of peptides to proteins without prior knowledge of the binding site

scientific article

Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study

scientific article published in February 2009

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes

scientific article

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes

scientific article published on 24 December 2015

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase.

scientific article

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

scientific article published on 12 April 2018

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

scientific article

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

scientific article published on 7 December 2011

Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton.

scientific article

GROMACS 3.0: a package for molecular simulation and trajectory analysis

article

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

scientific article

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

scientific article (publication date: March 2008)

GROMACS molecule & liquid database

scientific article

GROMACS: A message-passing parallel molecular dynamics implementation

scientific article published in September 1995

GROMACS: fast, flexible, and free

scientific article (publication date: December 2005)

Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization

scientific article published on 8 October 2015

Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

article

Impact of sludge deposition on biodiversity

scientific article published on 30 August 2015

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

scientific article published on 12 May 2015

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.

scientific article published in June 2018

Large influence of cholesterol on solute partitioning into lipid membranes

scientific article

Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

article by Mohammad M. Ghahremanpour et al published 21 September 2016 in Journal of Chemical Physics

Local partition coefficients govern solute permeability of cholesterol-containing membranes

scientific article published on December 2013

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

scientific article published on 19 December 2019

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.

scientific article published on 22 November 2013

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

scientific article published on 10 November 2017

Mobility-based prediction of hydration structures of protein surfaces

scientific article

Model for the dynamics of a water cluster in an x-ray free electron laser beam

scientific article published on 11 November 2004

Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.

scientific article

Molecular dynamics simulations of a membrane protein-micelle complex in vacuo

scientific article published in November 2009

Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon

scientific article

Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics

scientific article published on 01 August 2019

Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding

scientific article published on 8 September 2010

Phase-Transferable Force Field for Alkali Halides

Polarizable Drude Model with s-type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

scientific article published on 12 August 2019

Probing ¹³C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity

scientific article published on 4 March 2011

Protein structures under electrospray conditions

scientific article

Proteins, lipids, and water in the gas phase

scientific article

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations

scientific article published on 29 September 2005

Rotational and Translational Diffusion of Proteins as a Function of Concentration

scientific article published on 27 November 2019

Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids

scientific article

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

scientific article

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

article

Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP).

scientific article

Speeding up parallel GROMACS on high-latency networks

scientific article

Statistical efficiency of methods for computing free energy of hydration

article

Structural stability of electrosprayed proteins: temperature and hydration effects.

scientific article

Structural studies of melting on the picosecond time scale

scientific article

Structural variability and the incoherent addition of scattered intensities in single-particle diffraction

scientific article

Subunit Interface Dynamics in Hexadecameric Rubisco ⬇️

scientific article published on July 6, 2011

Systematic exploration of multiple drug binding sites

scientific article

Systematically improved melting point prediction: a detailed physical simulation model is required

scientific article published on 01 October 2019

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

scientific article published in January 2019

The Alexandria library, a quantum-chemical database of molecular properties for force field development

scientific article

Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media

scientific article published in March 2006

Thermodynamics of hydronium and hydroxide surface solvation

Thiamin function, metabolism, uptake, and transport

scientific article published on 31 January 2014

Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin

scientific article

Toward prediction of functional protein pockets using blind docking and pocket search algorithms ⬇️

scientific article published on March 30, 2011

Trajectory NG: portable, compressed, general molecular dynamics trajectories

scientific article published on 26 January 2011

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

scientific article

Transient isomers in the photodissociation of bromoiodomethane

scientific article published in April 2018

Virus capsid dissolution studied by microsecond molecular dynamics simulations

scientific article

Water Determines the Structure and Dynamics of Proteins

scientific article

List of works by David van der Spoel

A potential for molecular simulation of compounds with linear moieties

A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins

A temperature predictor for parallel tempering simulations

A theoretical study of repeating sequence in HRP II: a combination of molecular dynamics simulations and (17)O quadrupole coupling tensors

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

Anopheles gambiae, Anoga-HrTH hormone, free and bound structure--a nuclear magnetic resonance experiment

Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

Atomistic simulation of ion solvation in water explains surface preference of halides.

Binding of Pollutants to Biomolecules: A Simulation Study

Blind docking of drug-sized compounds to proteins with up to a thousand residues

Chemical properties, environmental fate, and degradation of seven classes of pollutants

Coherent diffraction of a single virus particle: The impact of a water layer on the available orientational information ⬇️

Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents

Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations

Deciphering solution scattering data with experimentally guided molecular dynamics simulations

Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin

Efficient docking of peptides to proteins without prior knowledge of the binding site

Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo: a simulation study

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes

Fluorescence probe of Trp-cage protein conformation in solution and in gas phase.

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton.

GROMACS 3.0: a package for molecular simulation and trajectory analysis

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

GROMACS molecule & liquid database

GROMACS: A message-passing parallel molecular dynamics implementation

GROMACS: fast, flexible, and free

Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents: Cyclodextrin Dimerization

Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

Impact of sludge deposition on biodiversity

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.

Large influence of cholesterol on solute partitioning into lipid membranes

Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

Local partition coefficients govern solute permeability of cholesterol-containing membranes

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.

Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

Mobility-based prediction of hydration structures of protein surfaces

Model for the dynamics of a water cluster in an x-ray free electron laser beam

Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.

Molecular dynamics simulations of a membrane protein-micelle complex in vacuo

Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon

Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics

Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding

Phase-Transferable Force Field for Alkali Halides

Polarizable Drude Model with s-type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

Probing ¹³C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity

Protein structures under electrospray conditions

Proteins, lipids, and water in the gas phase

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations

Rotational and Translational Diffusion of Proteins as a Function of Concentration

Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids

Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP).

Speeding up parallel GROMACS on high-latency networks

Statistical efficiency of methods for computing free energy of hydration

Structural stability of electrosprayed proteins: temperature and hydration effects.

Structural studies of melting on the picosecond time scale

Structural variability and the incoherent addition of scattered intensities in single-particle diffraction

Subunit Interface Dynamics in Hexadecameric Rubisco ⬇️

Systematic exploration of multiple drug binding sites

Systematically improved melting point prediction: a detailed physical simulation model is required

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

The Alexandria library, a quantum-chemical database of molecular properties for force field development

Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media

Thermodynamics of hydronium and hydroxide surface solvation

Thiamin function, metabolism, uptake, and transport

Time-resolved WAXS reveals accelerated conformational changes in iodoretinal-substituted proteorhodopsin

Toward prediction of functional protein pockets using blind docking and pocket search algorithms ⬇️

Trajectory NG: portable, compressed, general molecular dynamics trajectories

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models