David van der Spoel

Orcid: 0000-0002-7659-8526

According to our database1, David van der Spoel authored at least 22 papers between 2003 and 2023.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

Legend:

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PhD thesis 
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Links

Online presence:

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Bibliography

2023
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.
J. Chem. Inf. Model., January, 2023

2020
Toward a Computational Ecotoxicity Assay.
J. Chem. Inf. Model., 2020

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation.
J. Chem. Inf. Model., 2020

2019
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems.
PLoS Comput. Biol., 2019

2018
Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models.
J. Chem. Inf. Model., 2018

2017
Systematic exploration of multiple drug binding sites.
J. Cheminformatics, 2017

2016
Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes.
J. Chem. Inf. Model., 2016

Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.
J. Chem. Inf. Model., 2016

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes.
J. Chem. Inf. Model., 2016

2015
Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.
J. Chem. Inf. Model., 2015

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model.
J. Comput. Chem., 2015

Mobility-based prediction of hydration structures of protein surfaces.
Bioinform., 2015

2014
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations.
J. Comput. Chem., 2014

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program.
Bioinform., 2014

2013
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Bioinform., 2013

2012
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations.
PLoS Comput. Biol., 2012

GROMACS molecule & liquid database.
Bioinform., 2012

2007
Speeding up parallel GROMACS on high-latency networks.
J. Comput. Chem., 2007

2006
Improved GROMACS Scaling on Ethernet Switched Clusters.
Proceedings of the Recent Advances in Parallel Virtual Machine and Message Passing Interface, 2006

Protein Folding Properties from Molecular Dynamics Simulations.
Proceedings of the Applied Parallel Computing. State of the Art in Scientific Computing, 2006

2005
GROMACS: Fast, flexible, and free.
J. Comput. Chem., 2005

2003
Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10.
J. Comput. Aided Mol. Des., 2003


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