Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10. - Sergio Manzetti; Daniel R. McCulloch; Adrian C. Herington; David van der Spoel (J. Comput. Aided Mol. Des., 2003)

GROMACS: Fast, flexible, and free. - David van der Spoel; Erik Lindahl; Berk Hess; Gerrit Groenhof; Alan E. Mark; Herman J. C. Berendsen (J. Comput. Chem., 2005)

Protein Folding Properties from Molecular Dynamics Simulations. - David van der Spoel; Alexandra Patriksson; M. Marvin Seibert (PARA, 2006)

Improved GROMACS Scaling on Ethernet Switched Clusters. - Carsten Kutzner; David van der Spoel; Martin Fechner; Erik Lindahl; Udo W. Schmitt; Bert L. de Groot; Helmut Grubmüller (PVM/MPI, 2006)

Speeding up parallel GROMACS on high-latency networks. - Carsten Kutzner; David van der Spoel; Martin Fechner; Erik Lindahl; Udo W. Schmitt; Bert L. de Groot; Helmut Grubmüller (J. Comput. Chem., 2007)

GROMACS molecule & liquid database. - David van der Spoel; Paul J. van Maaren; Carl Caleman (Bioinform., 2012)

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations. - Daniel S. D. Larsson; Lars Liljas; David van der Spoel (PLoS Comput. Biol., 2012)

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

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. - Mohammad Mehdi Ghahremanpour; Seyed Shahriar Arab; Saman Biook Aghazadeh; Jin Zhang 032; David van der Spoel (Bioinform., 2014)

An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. - Magnus Lundborg; Rossen Apostolov; Daniel Spångberg; Anders Gärdenäs; David van der Spoel; Erik Lindahl (J. Comput. Chem., 2014)

Mobility-based prediction of hydration structures of protein surfaces. - Norbert Jeszenoi; István Horváth; Mónika Bálint; David van der Spoel; Csaba Hetényi (Bioinform., 2015)

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. - Justin A. Lemkul; Benoît Roux; David van der Spoel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2015)

Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. - Jin Zhang 032; Badamkhatan Tuguldur; David van der Spoel (J. Chem. Inf. Model., 2015)

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes. - Norbert Jeszenoi; Mónika Bálint; István Horváth; David van der Spoel; Csaba Hetényi (J. Chem. Inf. Model., 2016)

Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. - Jin Zhang 032; Badamkhatan Tuguldur; David van der Spoel (J. Chem. Inf. Model., 2016)

Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes. - Haiyang Zhang 003; Chunhua Yin; Hai Yan; David van der Spoel (J. Chem. Inf. Model., 2016)

Systematic exploration of multiple drug binding sites. - Mónika Bálint; Norbert Jeszenoi; István Horváth; David van der Spoel; Csaba Hetényi (J. Cheminformatics, 2017)

Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models. - Haiyang Zhang 003; Chunhua Yin; Yang Jiang 004; David van der Spoel (J. Chem. Inf. Model., 2018)

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems. - Arne Elofsson; Berk Hess; Erik Lindahl; Alexey Onufriev; David van der Spoel; Anders Wallqvist (PLoS Comput. Biol., 2019)

Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation. - Leandro Oliveira Bortot; Zahedeh Bashardanesh; David van der Spoel (J. Chem. Inf. Model., 2020)

Toward a Computational Ecotoxicity Assay. - Natasha Kamerlin; Mickaël G. Delcey; Sergio Manzetti; David van der Spoel (J. Chem. Inf. Model., 2020)

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation. - Kristian Kríz; Lisa Schmidt; Alfred T. Andersson; Marie-Madeleine Walz; David van der Spoel (J. Chem. Inf. Model., 2023)