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ORCIDDavid van der Spoel
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2020 – today
- 2023
[j20]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): 412-431 (2023)- 2020
- [j19]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): 322-331 (2020) - [j18]Natasha Kamerlin, Mickaël G. Delcey, Sergio Manzetti, David van der Spoel:
Toward a Computational Ecotoxicity Assay. J. Chem. Inf. Model. 60(8): 3792-3803 (2020)
2010 – 2019
- 2019
- [j17]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) - 2018
- [j16]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): 1037-1052 (2018) - 2017
- [j15]Mónika Bálint, Norbert Jeszenoi, István Horváth, David van der Spoel, Csaba Hetényi:
Systematic exploration of multiple drug binding sites. J. Cheminformatics 9(1): 65:1-65:12 (2017) - 2016
- [j14]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): 148-158 (2016) - [j13]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): 819-820 (2016) - [j12]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): 2080-2092 (2016) - 2015
- [j11]Norbert Jeszenoi, István Horváth, Mónika Bálint, David van der Spoel, Csaba Hetényi:
Mobility-based prediction of hydration structures of protein surfaces. Bioinform. 31(12): 1959-1965 (2015) - [j10]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): 1473-1479 (2015) - [j9]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): 1192-1201 (2015) - 2014
- [j8]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): 439-441 (2014) - [j7]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): 260-269 (2014) - 2013
- [j6]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): 845-854 (2013) - 2012
- [j5]David van der Spoel, Paul J. van Maaren, Carl Caleman:
GROMACS molecule & liquid database. Bioinform. 28(5): 752-753 (2012) - [j4]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)
2000 – 2009
- 2007
- [j3]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): 2075-2084 (2007) - 2006
- [c2]David van der Spoel, Alexandra Patriksson, M. Marvin Seibert:
Protein Folding Properties from Molecular Dynamics Simulations. PARA 2006: 109-115 - [c1]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: 404-405 - 2005
- [j2]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): 1701-1718 (2005) - 2003
- [j1]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): 551-565 (2003)
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