David van der Spoel

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 12

Top Topics

Trajectory Data

Biological Systems

Simulation Models

Top Venues

J. Chem. Inf. Model.

J. Comput. Chem.

J. Cheminformatics

Publications

Kristian Kríz, Lisa Schmidt, Alfred T. Andersson, Marie-Madeleine Walz, David van der Spoel
An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. J. Chem. Inf. Model. 63 (2) (2023)
Leandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel
Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. J. Chem. Inf. Model. 60 (1) (2020)
Natasha Kamerlin, Mickaël G. Delcey, Sergio Manzetti, David van der Spoel
Toward a Computational Ecotoxicity Assay. J. Chem. Inf. Model. 60 (8) (2020)
Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist
Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. PLoS Comput. Biol. 15 (1) (2019)
Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel
Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. J. Chem. Inf. Model. 58 (5) (2018)
Mónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi
Systematic exploration of multiple drug binding sites. J. Cheminformatics 9 (1) (2017)
Haiyang Zhang, Chunhua Yin, Hai Yan, David van der Spoel
Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes. J. Chem. Inf. Model. 56 (10) (2016)
Jin Zhang, Badamkhatan Tuguldur, David van der Spoel
Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J. Chem. Inf. Model. 56 (4) (2016)
Norbert Jeszenoi, Mónika Bálint, István Horváth, David van der Spoel, Csaba Hetényi
Exploration of Interfacial Hydration Networks of Target-Ligand Complexes. J. Chem. Inf. Model. 56 (1) (2016)
Jin Zhang, Badamkhatan Tuguldur, David van der Spoel
Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J. Chem. Inf. Model. 55 (6) (2015)
Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J. Comput. Chem. 36 (19) (2015)
Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi
Mobility-based prediction of hydration structures of protein surfaces. Bioinform. 31 (12) (2015)
Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel, Erik Lindahl
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. J. Comput. Chem. 35 (3) (2014)
Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang, David van der Spoel
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. Bioinform. 30 (3) (2014)
Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinform. 29 (7) (2013)
David van der Spoel, Paul J. van Maaren, Carl Caleman
GROMACS molecule & liquid database. Bioinform. 28 (5) (2012)
Daniel S. D. Larsson, Lars Liljas, David van der Spoel
Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations. PLoS Comput. Biol. 8 (5) (2012)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Speeding up parallel GROMACS on high-latency networks. J. Comput. Chem. 28 (12) (2007)
David van der Spoel, Alexandra Patriksson, M. Marvin Seibert
Protein Folding Properties from Molecular Dynamics Simulations. PARA (2006)
Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot, Helmut Grubmüller
Improved GROMACS Scaling on Ethernet Switched Clusters. PVM/MPI (2006)
David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark, Herman J. C. Berendsen
GROMACS: Fast, flexible, and free. J. Comput. Chem. 26 (16) (2005)
Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington, David van der Spoel
Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. J. Comput. Aided Mol. Des. 17 (9) (2003)