David Van der Spoel

Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 5435-5447, 2026

• DOI för Bayesian Modeling of Polarizable Water: Lessons for Force Field Development
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Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models

Hosseini, A. Najla; Kriz, Kristian; Van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 2220-2231, 2026

• DOI för Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models
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plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output

Rosenbaum, Måns; Van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 2955-2959, 2026

• DOI för plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output
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LacI strikes a balance between stability and inducibility

Yuan, Jinwen; Lüking, Malin; Zikrin, Spartak; Sen, Beer Chakra et al.

Ingår i Nucleic Acids Research, 2026

• DOI för LacI strikes a balance between stability and inducibility
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Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space

Van der Spoel, David; Marrades, Julián; Kriz, Kristian; Hosseini, A. Najla et al.

Ingår i Digital Discovery, s. 1925-1935, 2025

• DOI för Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space
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Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Nordman, Alfred T.; Engblom, Stefan; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 5435-5447, 2026

• DOI för Bayesian Modeling of Polarizable Water: Lessons for Force Field Development
• Ladda ner fulltext (pdf) av Bayesian Modeling of Polarizable Water: Lessons for Force Field Development

Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models

Hosseini, A. Najla; Kriz, Kristian; Van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 2220-2231, 2026

• DOI för Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models
• Ladda ner fulltext (pdf) av Beyond Partitioning: Using Force Field Science to Evaluate Electrostatics Models

plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output

Rosenbaum, Måns; Van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 2955-2959, 2026

• DOI för plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output
• Ladda ner fulltext (pdf) av plotXVG: Batch Generation of Publication-Quality Graphs from GROMACS Output

LacI strikes a balance between stability and inducibility

Yuan, Jinwen; Lüking, Malin; Zikrin, Spartak; Sen, Beer Chakra et al.

Ingår i Nucleic Acids Research, 2026

• DOI för LacI strikes a balance between stability and inducibility
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Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space

Van der Spoel, David; Marrades, Julián; Kriz, Kristian; Hosseini, A. Najla et al.

Ingår i Digital Discovery, s. 1925-1935, 2025

• DOI för Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space
• Ladda ner fulltext (pdf) av Evolutionary machine learning of physics-based force fields in high-dimensional parameter-space

Bayesian three-point water models

Nordman, Alfred T.; Engblom, Stefan; Van der Spoel, David

Ingår i npj Computational Materials, 2025

• DOI för Bayesian three-point water models
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The need to implement FAIR principles in biomolecular simulations

Amaro, Rommie E.; Åqvist, Johan; Bahar, Ivet; Battistini, Federica et al.

Ingår i Nature Methods, s. 641-645, 2025

• DOI för The need to implement FAIR principles in biomolecular simulations

Point + Gaussian charge model for electrostatic interactions derived by machine learning

Van der Spoel, David; Hosseini, A. Najla

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 13817-13820, 2025

• DOI för Point + Gaussian charge model for electrostatic interactions derived by machine learning
• Ladda ner fulltext (pdf) av Point + Gaussian charge model for electrostatic interactions derived by machine learning

Quantitative evaluation of anharmonic bond potentials for molecular simulations

van Maaren, Paul J.; Van der Spoel, David

Ingår i Digital Discovery, s. 824-830, 2025

• DOI för Quantitative evaluation of anharmonic bond potentials for molecular simulations
• Ladda ner fulltext (pdf) av Quantitative evaluation of anharmonic bond potentials for molecular simulations

Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields

Kriz, Kristian; Van der Spoel, David

Ingår i The Journal of Physical Chemistry Letters, s. 9974-9978, 2024

• DOI för Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields
• Ladda ner fulltext (pdf) av Quantification of Anisotropy in Exchange and Dispersion Interactions: A Simple Model for Physics-Based Force Fields

Assessment of Climate Impact of Sustainable Forestry Based on Landscape Structure

Prytz, Kjell; Van der Spoel, David

Ingår i Forests, 2024

• DOI för Assessment of Climate Impact of Sustainable Forestry Based on Landscape Structure
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Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?

Hosseini, A. Najla; van der Spoel, David

Ingår i The Journal of Physical Chemistry Letters, s. 1079-1088, 2024

• DOI för Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
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Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases

Kriz, Kristian; van Maaren, Paul J.; Van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 2362-2376, 2024

• DOI för Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases
• Ladda ner fulltext (pdf) av Impact of Combination Rules, Level of Theory, and Potential Function on the Modeling of Gas- and Condensed-Phase Properties of Noble Gases

Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

Schmidt, Lisa; Van der Spoel, David; Walz, Marie-Madeleine

Ingår i ACS Physical Chemistry Au, s. 84-93, 2023

• DOI för Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations
• Ladda ner fulltext (pdf) av Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations

Can molecular dynamics be used to simulate biomolecular recognition?

Lüking, Malin; Van der Spoel, David; Elf, Johan; Tribello, Gareth A. A.

Ingår i Journal of Chemical Physics, 2023

• DOI för Can molecular dynamics be used to simulate biomolecular recognition?

Simulations of Amyloid-Forming Peptides in the Crystal State

Hosseini, A. Najla; Van der Spoel, David

Ingår i The Protein Journal, s. 192-204, 2023

• DOI för Simulations of Amyloid-Forming Peptides in the Crystal State
• Ladda ner fulltext (pdf) av Simulations of Amyloid-Forming Peptides in the Crystal State

Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

Balint, Monika; Zsido, Balazs Zoltan; Van der Spoel, David; Hetenyi, Csaba

Ingår i International Journal of Molecular Sciences, 2022

• DOI för Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design
• Ladda ner fulltext (pdf) av Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

Classical molecular dynamics

Brooks, Charles L.; Case, David A.; Plimpton, Steve; Roux, Benoit et al.

Ingår i Journal of Chemical Physics, 2021

• DOI för Classical molecular dynamics

Editorial overview: Theory and simulation and their new friends

Shehu, Amarda; Van der Spoel, David

Ingår i Current opinion in structural biology, 2021

• DOI för Editorial overview: Theory and simulation and their new friends

NMR Refinement and Peptide Folding Using the GROMACS Software

Sinelnikova, Anna; Van der Spoel, David

Ingår i Journal of Biomolecular NMR, s. 143-149, 2021

• DOI för NMR Refinement and Peptide Folding Using the GROMACS Software
• Ladda ner fulltext (pdf) av NMR Refinement and Peptide Folding Using the GROMACS Software

The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

Assis Silva, Flavia Cristina; Lourenco, Tuanan da Costa; Van der Spoel, David; Aparicio, Santiago et al.

Ingår i Journal of Chemical Physics, 2021

• DOI för The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

Microscopic origins of conductivity in molten salts unraveled by computer simulations

Walz, Marie-Madeleine; Van der Spoel, David

Ingår i Communications Chemistry, 2021

• DOI för Microscopic origins of conductivity in molten salts unraveled by computer simulations
• Ladda ner fulltext (pdf) av Microscopic origins of conductivity in molten salts unraveled by computer simulations

Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

Gapsys, Vytautas; Yildirim, Ahmet; Aldeghi, Matteo; Khalak, Yuriy et al.

Ingår i Communications Chemistry, 2021

• DOI för Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches
• Ladda ner fulltext (pdf) av Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

Henschel, Henning; Andersson, Alfred T.; Jespers, Willem; Ghahremanpour, Mohammad Mehdi et al.

Ingår i Journal of Chemical Theory and Computation, s. 3307-3315, 2020

• DOI för Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields
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Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

Bortot, Leandro Oliveira; Bashardanesh, Zahedeh; Van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 322-331, 2020

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

An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Henschel, Henning; Van der Spoel, David

Ingår i The Journal of Physical Chemistry Letters, s. 5471-5475, 2020

• DOI för An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra
• Ladda ner fulltext (pdf) av An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Propagation of uncertainty in physicochemical data to force field predictions

Yildirim, Ahmet; Ghahremanpour, Mohammad Mehdi; Van der Spoel, David

Ingår i Physical Review Research, 2020

• DOI för Propagation of uncertainty in physicochemical data to force field predictions
• Ladda ner fulltext (pdf) av Propagation of uncertainty in physicochemical data to force field predictions

Toward a Computational Ecotoxicity Assay

Kamerlin, Natasha; Delcey, Mickaël G; Manzetti, Sergio; Van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 3792-3803, 2020

• DOI för Toward a Computational Ecotoxicity Assay

A potential for molecular simulation of compounds with linear moieties

Van der Spoel, David; Henschel, Henning; van Maaren, Paul J.; Ghahremanpour, Mohammad M. et al.

Ingår i Journal of Chemical Physics, 2020

• DOI för A potential for molecular simulation of compounds with linear moieties
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Rotational and Translational Diffusion of Proteins as a Function of Concentration

Bashardanesh, Zahedeh; Elf, Johan; Zhang, Haiyang; Van der Spoel, David

Ingår i ACS Omega, s. 20654-20664, 2019

• DOI för Rotational and Translational Diffusion of Proteins as a Function of Concentration
• Ladda ner fulltext (pdf) av Rotational and Translational Diffusion of Proteins as a Function of Concentration

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

Elofsson, Arne; Hess, Berk; Lindahl, Erik; Onufriev, Alexey et al.

Ingår i PloS Computational Biology, 2019

• DOI för Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
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Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

Van der Spoel, David; Manzetti, Sergio; Haiyang, Zhang; Klamt, Andreas

Ingår i ACS Omega, s. 13772-13781, 2019

• DOI för Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods
• Ladda ner fulltext (pdf) av Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

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

Walz, Marie-Madeleine; Van der Spoel, David

Ingår i Chemical Communications, s. 12044-12047, 2019

• DOI för Systematically improved melting point prediction: a detailed physical simulation model is required
• Ladda ner fulltext (pdf) av Systematically improved melting point prediction: a detailed physical simulation model is required

Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts

Walz, Marie-Madeleine; Van der Spoel, David

Ingår i The Journal of Physical Chemistry C, s. 25596-25602, 2019

• DOI för Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts

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

Walz, Marie-Madeleine; Van der Spoel, David

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 18516-18524, 2019

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

Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

Yin, Chunhua; Cui, Ziheng; Jiang, Yang; Van der Spoel, David et al.

Ingår i The Journal of Physical Chemistry C, s. 17745-17756, 2019

• DOI för Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

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

Fischer, Nina M.; Poleto, Marcelo D.; Steuer, Jakob; van der Spoel, David

Ingår i Nucleic Acids Research, s. 4872-4882, 2018

• DOI för Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
• Ladda ner fulltext (pdf) av Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations

Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

Bashardanesh, Zahedeh; van der Spoel, David

Ingår i Journal of Physical Chemistry B, s. 8018-8027, 2018

• DOI för Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

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

Ghahremanpour, Mohammad Mehdi; van Maaren, Paul J.; Caleman, Carl; Hutchison, Geoffrey R. et al.

Ingår i Journal of Chemical Theory and Computation, s. 5553-5566, 2018

• DOI för Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields

Phase-Transferable Force Field for Alkali Halides

Walz, Marie-Madeleine; Ghahremanpour, Mohammad M.; van Maaren, Paul J.; Van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 5933-5948, 2018

• DOI för Phase-Transferable Force Field for Alkali Halides

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

Ghahremanpour, Mohammad M.; van Maaren, Paul J; Van der Spoel, David

Ingår i Scientific Data, 2018

• DOI för The Alexandria library, a quantum-chemical database of molecular properties for force field development
• Ladda ner fulltext (pdf) av The Alexandria library, a quantum-chemical database of molecular properties for force field development

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Van der Spoel, David; Ghahremanpour, Mohammad M.; Lemkul, Justin A.

Ingår i Journal of Physical Chemistry A, s. 8982-8988, 2018

• DOI för Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Statistical efficiency of methods for computing free energy of hydration

Yildirim, Ahmet; Wassenaar, Tsjerk A.; Van der Spoel, David

Ingår i Journal of Chemical Physics, 2018

• DOI för Statistical efficiency of methods for computing free energy of hydration
• Ladda ner fulltext (pdf) av Statistical efficiency of methods for computing free energy of hydration

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

Zhang, Haiyang; Yin, Chunhua; Jiang, Yang; van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 1037-1052, 2018

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

Transient isomers in the photodissociation of bromoiodomethane

Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas et al.

Ingår i Journal of Chemical Physics, 2018

• DOI för Transient isomers in the photodissociation of bromoiodomethane

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

dos Santos Soares, Ricardo de Oliveira; Bortot, Leandro Oliveira; van Der Spoel, David; Caliri, Antonio

Ingår i Journal of Physics, 2017

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

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

Zhang, Haiyang; Jiang, Yang; Yan, Hai; Yin, Chunhua et al.

Ingår i The Journal of Physical Chemistry Letters, s. 2705-2712, 2017

• DOI för Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton

Systematic exploration of multiple drug binding sites

Bálint, Mónika; Jeszenői, Norbert; Horváth, István; van der Spoel, David et al.

Ingår i Journal of Cheminformatics, 2017

• DOI för Systematic exploration of multiple drug binding sites
• Ladda ner fulltext (pdf) av Systematic exploration of multiple drug binding sites

Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

Lehmann, Laura C.; Hewitt, Graeme; Aibara, Shintaro; Leitner, Alexander et al.

Ingår i Molecular Cell, s. 847-8590000000, 2017

• DOI för Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1
• Ladda ner fulltext (pdf) av Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

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

Zhang, Jin; Zhang, Haiyang; Wu, Tao; Wang, Qi et al.

Ingår i Journal of Chemical Theory and Computation, s. 1034-1043, 2017

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

Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

Zhang, Haiyang; Lv, Yongqin; Tan, Tianwei; van der Spoel, David

Ingår i Journal of Physical Chemistry B, s. 477-484, 2016

• DOI för Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

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

Ghahremanpour, Mohammad Mehdi; van Maaren, Paul J.; Ditz, Jonas C.; Lindh, Roland et al.

Ingår i Journal of Chemical Physics, 2016

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

Binding of Pollutants to Biomolecules: A Simulation Study

Yildirim, Ahmet; Zhang, Jin; Manzetti, Sergio; van der Spoel, David

Ingår i Chemical Research in Toxicology, s. 1679-1688, 2016

• DOI för Binding of Pollutants to Biomolecules: A Simulation Study
• Ladda ner fulltext (pdf) av Binding of Pollutants to Biomolecules: A Simulation Study

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

Zhang, Haiyang; Yin, Chunhua; Yan, Hai; van der Spoel, David

Ingår i Journal of Chemical Information and Modeling, s. 2080-2092, 2016

• DOI för Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes
• Ladda ner fulltext (pdf) av Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes

Exploration of Interfacial Hydration Networks of Target Ligand Complexes

Jeszenoi, Norbert; Balint, Monika; Horvath, Istvan; van der Spoel, David et al.

Ingår i Journal of Chemical Information and Modeling, s. 148-158, 2016

• DOI för Exploration of Interfacial Hydration Networks of Target Ligand Complexes

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

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; Ditz, Jonas C.; Lindh, Roland et al.

Ingår i Journal of Chemical Physics, 2016

• DOI för Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity
• Ladda ner fulltext (pdf) av Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

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

Nasedkin, Alexandr; Marcellini, Moreno; Religa, Tomasz L.; Freund, Stefan M. et al.

Ingår i PLOS ONE, 2015

• DOI för Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation
• Ladda ner fulltext (pdf) av Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

Mobility-based prediction of hydration structures of protein surfaces

Jeszenoi, Norbert; Horvath, Istvan; Balint, Monika; van der Spoel, David et al.

Ingår i Bioinformatics, s. 1959-1965, 2015

• DOI för Mobility-based prediction of hydration structures of protein surfaces

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

Zhang, Jin; Tuguldur, Badamkhatan; van der Spoel, David

Ingår i JOURNAL OF CHEMICAL INFORMATION AND MODELING, s. 1192-1201, 2015

• DOI för Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation

Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

Bjorling, Alexander; Niebling, Stephan; Marcellini, Moreno; van der Spoel, David et al.

Ingår i Journal of Chemical Theory and Computation, s. 780-787, 2015

• DOI för Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations
• Ladda ner fulltext (pdf) av Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

Behzadi, Hadi; Roonasi, Payman; Taghipour, Khatoon Assle; van der Spoel, David et al.

Ingår i Journal of Molecular Structure, s. 196-202, 2015

• DOI för Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study

Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model

Lemkul, Justin A.; Roux, Benoit; van der Spoel, David; MacKerell, Alexander D.

Ingår i Journal of Computational Chemistry, s. 1473-1479, 2015

• DOI för Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model

Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions

Fischer, Nina M.; van Maaren, Paul J.; Ditz, Jonas C.; Yildirim, Ahmet et al.

Ingår i Journal of Chemical Theory and Computation, s. 2938-2944, 2015

• DOI för Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions

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

Zhang, Haiyang; Tan, Tianwei; Van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 5103-5113, 2015

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

An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations

Lundborg, Magnus; Apostolov, Rossen; Spångberg, Daniel; Gardenäs, Anders et al.

Ingår i Journal of Computational Chemistry, s. 260-269, 2014

• DOI för An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations

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

Zhang, Haiyang; Tan, Tianwei; Hetenyi, Csaba; Lv, Yongqin et al.

Ingår i The Journal of Physical Chemistry C, s. 7163-7173, 2014

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

Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems

Saethre, Bjorn Steen; Hoffmann, Alex C.; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 5606-5615, 2014

• DOI för Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems

CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir

van Lun, Michiel; Hub, Jochen S.; van der Spoel, David; Andersson, Inger

Ingår i Journal of the American Chemical Society, s. 3165-3171, 2014

• DOI för CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir

Thiamin Function, Metabolism, Uptake, and Transport

Manzetti, Sergio; Zhang, Jin; van der Spoel, David

Ingår i Biochemistry, s. 821-835, 2014

• DOI för Thiamin Function, Metabolism, Uptake, and Transport

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

Ghahremanpour, Mohammad Mehdi; Arab, Seyed Shahriar; Aghazadeh, Saman Biook; Zhang, Jin et al.

Ingår i Bioinformatics, s. 439-441, 2014

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

Thermodynamics of hydronium and hydroxide surface solvation

Hub, Jochen S.; Wolf, Maarten G.; Caleman, Carl; van Maaren, Paul J. et al.

Ingår i Chemical Science, s. 1745-1749, 2014

• DOI för Thermodynamics of hydronium and hydroxide surface solvation

Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

Zhang, Haiyang; Tan, Tianwei; Hetenyi, Csaba; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 4542-4551, 2013

• DOI för Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

Unexpected Effects of Cholesterol on Membrane Permeability

Wennberg, Christian L.; Zocher, Florian; Van der Spoel, David; Pohl, Peter et al.

Ingår i Biophysical Journal, 2013

• DOI för Unexpected Effects of Cholesterol on Membrane Permeability

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

Pronk, Sander; Pall, Szilard; Schulz, Roland; Larsson, Per et al.

Ingår i Bioinformatics, s. 845-854, 2013

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

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

Mugumbate, Grace; Jackson, Graham E.; van der Spoel, David; Kövér, Katalin E. et al.

Ingår i Peptides, s. 94-100, 2013

• DOI för Anopheles gambiae, Anoga-HrTH hormone, free and bound structure: A nuclear magnetic resonance experiment

Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View

Lourenco, Tuanan C.; Coelho, Mariny F. C.; Ramalho, Teodorico C.; van der Spoel, David et al.

Ingår i Environmental Science and Technology, s. 7421-7429, 2013

• DOI för Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

Zocher, Florian; van der Spoel, David; Pohl, Peter; Hub, Jochen S.

Ingår i Biophysical Journal, s. 2760-2770, 2013

• DOI för Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

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

Marklund, Erik G.; Mahmutovic, Anel; Berg, Otto G.; Hammar, Petter et al.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 19796-19801, 2013

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

beta-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus

Munyuki, Gadzikano; Jackson, Graham E.; Venter, Gerhard A.; Koever, Katalin E. et al.

Ingår i Biochemistry, s. 7798-7806, 2013

• DOI för beta-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

Larsson, Daniel; Liljas, Lars; van der Spoel, David

Ingår i PloS Computational Biology, 2012

• DOI för Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations
• Ladda ner fulltext (pdf) av Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

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

Larsson, Daniel; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 2474-2483, 2012

• DOI för Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids

Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules

Zhang, Haiyang; Ge, Chunling; van der Spoel, David; Feng, Wei et al.

Ingår i Journal of Physical Chemistry B, s. 3880-3889, 2012

• DOI för Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules

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

Caleman, Carl; van Maaren, Paul J.; Hong, Minyan; Hub, Jochen S. et al.

Ingår i Journal of Chemical Theory and Computation, s. 61-74, 2012

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

Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation

Yang, Hongqian; Good, David M.; van der Spoel, David; Zubarev, Roman A.

Ingår i Journal of the American Society for Mass Spectrometry, s. 1319-1325, 2012

• DOI för Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation

Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil

Saethre, Bjorn Steen; van der Spoel, David; Hoffmann, Alex C.

Ingår i Journal of Physical Chemistry B, s. 5933-5940, 2012

• DOI för Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil

Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

Wennberg, Christian L.; van der Spoel, David; Hub, Jochen S.

Ingår i Journal of the American Chemical Society, s. 5351-5361, 2012

• DOI för Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

Molecular recognition in different environments: β-Cyclodextrin dimer formation in organic solvents

Zhang, H.; Tan, T.; Feng, W.; Van Der Spoel, David

Ingår i Journal of Physical Chemistry B, s. 12684-12693, 2012

• DOI för Molecular recognition in different environments: β-Cyclodextrin dimer formation in organic solvents

GROMACS molecule & liquid database

van der Spoel, David; van Maaren, Paul J.; Caleman, Carl

Ingår i Bioinformatics, s. 752-753, 2012

• DOI för GROMACS molecule & liquid database

Organic molecules on the surface of water droplets: an energetic perspective

Hub, Jochen; Caleman, Carl; van der Spoel, David

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 9537-9545, 2012

• DOI för Organic molecules on the surface of water droplets: an energetic perspective

Trajectory NG: portable, compressed, general molecular dynamics trajectories

Spångberg, Daniel; Larsson, Daniel; van der Spoel, David

Ingår i Journal of Molecular Modeling, s. 2669-2685, 2011

• DOI för Trajectory NG: portable, compressed, general molecular dynamics trajectories

Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information

Wang, F; Weckert, E; Ziaja, B; Larsson, Daniel S.D. et al.

Ingår i Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2011

• DOI för Coherent Diffraction of a Single Virus Particle : The Impact of a Water Layer on the Available Orientational Information

Proteins, Lipids, and Water in the Gas Phase

van der Spoel, David; Marklund, Erik G.; Larsson, Daniel S. D.; Caleman, Carl

Ingår i Macromolecular Bioscience, s. 50-59, 2011

• DOI för Proteins, Lipids, and Water in the Gas Phase

GROMACS: the road ahead

van der Spoel, David; Hess, Berk

Ingår i WIREs Computational Molecular Science, s. 710-715, 2011

• DOI för GROMACS: the road ahead

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

Hetenyi, Csaba; van der Spoel, David

Ingår i Protein Science, s. 880-893, 2011

• DOI för Toward prediction of functional protein pockets using blind docking and pocket search algorithms

Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

Malmerberg, Erik; Omran, Ziad; Hub, Jochen S.; Li, Xuewen et al.

Ingår i Biophysical Journal, s. 1345-1353, 2011

• DOI för Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin

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

Caleman, Carl; Hub, Jochen S.; van Maaren, Paul J.; van der Spoel, David

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 6838-6842, 2011

• DOI för Atomistic simulation of ion solvation in water explains surface preference of halides

Subunit Interface Dynamics in Hexadecameric Rubisco

van Lun, Michiel; van der Spoel, David; Andersson, Inger

Ingår i Journal of Molecular Biology, s. 1083-1098, 2011

• DOI för Subunit Interface Dynamics in Hexadecameric Rubisco

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

Mugumbate, Grace; Jackson, Graham E.; van der Spoel, David

Ingår i Peptides, s. 553-559, 2011

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

On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

Caleman, Carl; Huldt, Gösta; Maia, Filipe R. N. C.; Ortiz, Carlos et al.

Ingår i ACS Nano, s. 139-146, 2011

• DOI för On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses

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

Behzadi, Hadi; Olyai, Mohamad Reza Talei Bavil; van der Spoel, David

Ingår i Journal of Molecular Modeling, s. 3289-3297, 2011

• DOI för Probing (13)C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity

Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

Lange, Oliver F.; van der Spoel, David; de Groot, Bert L.

Ingår i Biophysical Journal, s. 647-655, 2010

• DOI för Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data

g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Hub, Jochen S.; de Groot, Bert L.; van der Spoel, David

Ingår i Journal of Chemical Theory and Computation, s. 3713-3720, 2010

• DOI för g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

Hawk: the image reconstruction package for coherent X-ray diffractive imaging

Maia, Filipe R. N. C.; Ekeberg, Tomas; van der Spoel, David; Hajdu, Janos

Ingår i Journal of applied crystallography, s. 1535-1539, 2010

• DOI för Hawk: the image reconstruction package for coherent X-ray diffractive imaging

Structural stability of electrosprayed proteins: temperature and hydration effects

Marklund, Erik G.; Larsson, Daniel S. D.; van der Spoel, David; Patriksson, Alexandra et al.

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 8069-8078, 2009

• DOI för Structural stability of electrosprayed proteins: temperature and hydration effects

Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo

Friemann, Rosmarie; Larsson, Daniel S. D.; Wang, Yaofeng; van der Spoel, David

Ingår i Journal of the American Chemical Society, s. 16606-16607, 2009

• DOI för Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo

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

Wang, Yaofeng; Larsson, Daniel S D; van der Spoel, David

Ingår i Biochemistry, s. 1006-1015, 2009

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

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

Maia, Filipe R. N. C.; Ekeberg, Tomas; Timneanu, Nicusor; van der Spoel, David et al.

Ingår i Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2009

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

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

Jackson, Graham E; Mabula, Andre N; Stone, Shane R; Gäde, Gerd et al.

Ingår i Peptides, s. 557-564, 2009

• DOI för Solution conformations of an insect neuropeptide: crustacean cardioactive peptide (CCAP)

A density functional study of N-15 chemical shielding tensors in quinolines

Behzadi, Hadi; Esrafili, D; Beheshtian, Javad; Hadipour, L et al.

Ingår i Chemical Physics Letters, s. 196-200, 2009

• DOI för A density functional study of N-15 chemical shielding tensors in quinolines

A temperature predictor for parallel tempering simulations

Patriksson, Alexandra; van der Spoel, David

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 2073-2077, 2008

• DOI för A temperature predictor for parallel tempering simulations

Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex

Behzadi, Hadi; van der Spoel, David; Esrafili, Mehdi D; Parsafar, Gholam Abbas et al.

Ingår i Biophysical Chemistry, s. 200-206, 2008

• DOI för Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex

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

Behzadi, Hadi; Esrafili, Mehdi D; van der Spoel, David; Hadipour, Nasser L et al.

Ingår i Biophysical Chemistry, s. 76-80, 2008

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

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

Andersson, Magnus; Vincent, Jonathan; van der Spoel, David; Davidsson, Jan et al.

Ingår i Structure, s. 21-28, 2008

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

Picosecond Melting of Ice by an Infrared Laser Pulse

Caleman, Carl; van der Spoel, David

Ingår i Angewandte Chemie International Edition, s. 1417-1420, 2008

• DOI för Picosecond Melting of Ice by an Infrared Laser Pulse

GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Hess, Berk; Kutzner, Carsten; van der Spoel, David; Lindahl, Erik

Ingår i Journal of Chemical Theory and Computation, s. 435-447, 2008

• DOI för GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation

Proteins structures under electrospray conditions

Patriksson, Alexandra; Marklund, Erik; van der Spoel, David

Ingår i Biochemistry, s. 933-945, 2007

• DOI för Proteins structures under electrospray conditions

A direct comparison of protein structure in the gas and solution phase - the Trp-cage

Patriksson, Alexandra; Adams, Christopher M.; Kjeldsen, Frank; Zubarev, Roman et al.

Ingår i Journal of Physical Chemistry B, s. 13147-13150, 2007

• DOI för A direct comparison of protein structure in the gas and solution phase - the Trp-cage

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

Iavarone, A. T; Patriksson, Alexandra; van der Spoel, David; Parks, J. H.

Ingår i Journal of the American Chemical Society, s. 6726-6735, 2007

• DOI för Fluorescence probe of Trp-cage protein conformation in solution and in gas phase

Evaporation from water clusters containing singly charged ions

Caleman, Carl; van der Spoel, David

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 5105-5111, 2007

• DOI för Evaporation from water clusters containing singly charged ions

Speeding up parallel GROMACS on high-latency networks

Kutzner, Carsten; van der Spoel, David; Fechner, Martin; Lindahl, Erik et al.

Ingår i Journal of Computational Chemistry, s. 2075-2084, 2007

• DOI för Speeding up parallel GROMACS on high-latency networks

Energy Utilization, Catalysis and Evolution - Emergent Properties of Life

Szöke, Abraham; van der Spoel, David; Hajdu, Janos

Ingår i Current Chemical Biology, s. 53-57, 2007

• DOI för Energy Utilization, Catalysis and Evolution - Emergent Properties of Life

Protein folding kinetics and thermodynamics from atomistic simulations

van der Spoel, David; Seibert, M Marvin

Ingår i Physical Review Letters, s. 238102, 2006

• DOI för Protein folding kinetics and thermodynamics from atomistic simulations

Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques

Adams, Christopher; Kjeldsen, Frank; Patriksson, Alexandra; van Der Spoel, David et al.

Ingår i International Journal of Mass Spectrometry, s. 263-273, 2006

• DOI för Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques

Femtosecond diffractive imaging with a soft-X-ray free-electron laser

Chapman, Henry N.; Barty, Anton; Bogan, Michael J.; Boutet, Sebastien et al.

Ingår i Nature Physics, s. 839-843, 2006

• DOI för Femtosecond diffractive imaging with a soft-X-ray free-electron laser

Prediction of N-Ca Bond Cleavage Frequencies in Electron Capture Dissociation of Trp-cage Dications by Force-field Molecular Dynamics Simulations

Patriksson, Alexandra; Adams, Christopher; Kjeldsen, Frank; Raber, Johan et al.

Ingår i Int. J. Mass Spectrom., s. 124-135, 2006

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

Hetenyi, Csaba; van der Spoel, David

Ingår i FEBS Lett, s. 1447-50, 2006

The origin of layer structure artifacts in simulations of liquid water

Van Der Spoel, David; van Maaren, Paul

Ingår i J. Chem. Theor. Comp., s. 1-11, 2006

Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media.

van der Spoel, David; van Maaren, Paul J; Larsson, Per; Timneanu, Nicusor

Ingår i J Phys Chem B, s. 4393-8, 2006

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

Seibert, M Marvin; Patriksson, Alexandra; Hess, Berk; van der Spoel, David

Ingår i J Mol Biol, s. 173-83, 2005

GROMACS: fast, flexible, and free.

Van Der Spoel, David; Lindahl, Erik; Hess, Berk; Groenhof, Gerrit et al.

Ingår i J Comput Chem, s. 1701-18, 2005

Interactive visualization of electron density slices

Maia, Filipe; Szoke, Abraham; DeLano, Warren; van der Spoel, David

Ingår i J. Appl. Cryst., s. 563-565, 2005

Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb.

Gaffney, K J; Lindenberg, A M; Larsson, J; Sokolowski-Tinten, K et al.

Ingår i Phys Rev Lett, s. 125701, 2005

Clocking femtosecond X rays.

Cavalieri, A L; Fritz, D M; Lee, S H; Bucksbaum, P H et al.

Ingår i Phys Rev Lett, s. 114801, 2005

Atomic-scale visualization of inertial dynamics.

Lindenberg, A M; Larsson, J; Sokolowski-Tinten, K; Gaffney, K J et al.

Ingår i Science, s. 392-5, 2005

Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam

Bergh, Magnus; Timneanu, Nicusor; van der Spoel, David

Ingår i Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, 2004

Auger electron cascades in water and ice

Timneanu, Nicusor; Caleman, Carl; Hajdu, Janos; van der Spoel, David

Ingår i Chemical Physics, s. 277-283, 2004

• DOI för Auger electron cascades in water and ice

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

Shepherd, C. M.; van der Spoel, D; Vogel, H. J.

Ingår i J. Biomol. Struct. Dynam., s. 555-565, 2004

Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in complex with hypothetical substrates: New implications for catalysis and substrate affinity

Manzetti, Sergio; McCulloch, Daniel R; Herington, Adrian C.; Van Der Spoel, David

Ingår i Journal of Computer-Aided Molecular Design, s. 551-565, 2003

• DOI för Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in complex with hypothetical substrates: New implications for catalysis and substrate affinity

Dynamic properties of water/alcohol mixtures studied by computer simulation

Wensink, Erik; Hoffmann, Alex C.; van Maaren, Paul J; van der Spoel, D

Ingår i J. Chem. Phys., s. 7308-7317, 2003

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

Hetenyi, C; van der Spoel, D

Ingår i PROTEIN SCIENCE, s. 1729-1737, 2002

Space-time evolution of electron cascades in diamond

Ziaja, B; Szöke, A; van der Spoel, D; Hajdu, J

Ingår i PHYS REV B, 2002

GROMACS 3.0: a package for molecular simulation and trajectory analysis

Lindahl, E; Hess, B; van der Spoel, D

Ingår i JOURNAL OF MOLECULAR MODELING, s. 306-317, 2001

Molecular dynamics simulations of water with novel shell-model potentials

van Maaren, PJ; van der Spoel, D

Ingår i JOURNAL OF PHYSICAL CHEMISTRY B, s. 2618-2626, 2001

Potential for biomolecular imaging with femtosecond X-ray pulses

Neutze, R; Wouts, R; van der Spoel, D; Weckert, E et al.

Ingår i NATURE, s. 752-757, 2000

Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation

Tieleman, DP; van der Spoel, D; Berendsen, HJC

Ingår i JOURNAL OF PHYSICAL CHEMISTRY B, s. 6380-6388, 2000

The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters

van der Spoel, D

Ingår i BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE, s. 164-170, 1998

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Kříž, Kristian; Schmidt, Lisa; Andersson, Alfred T.; Walz, Marie-Madeleine et al.

Ingår i Journal of Chemical Information and Modeling, s. 412-431, 2023

• DOI för An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation
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Quantitative predictions from molecular simulations using explicit or implicit interactions

Van der Spoel, David; Zhang, Jin; Zhang, Haiyang

Ingår i WIREs Computational Molecular Science, 2022

• DOI för Quantitative predictions from molecular simulations using explicit or implicit interactions
• Ladda ner fulltext (pdf) av Quantitative predictions from molecular simulations using explicit or implicit interactions

Systematic design of biomolecular force fields

Van der Spoel, David

Ingår i Current opinion in structural biology, s. 18-24, 2021

• DOI för Systematic design of biomolecular force fields
• Ladda ner fulltext (pdf) av Systematic design of biomolecular force fields

Water Determines the Structure and Dynamics of Proteins

Bellissent-Funel, Marie-Claire; Hassanali, Ali; Havenith, Martina; Henchman, Richard et al.

Ingår i Chemical Reviews, s. 7673-7697, 2016

• DOI för Water Determines the Structure and Dynamics of Proteins

Impact of sludge deposition on biodiversity

Manzetti, Sergio; van der Spoel, David

Ingår i Ecotoxicology, s. 1799-1814, 2015

• DOI för Impact of sludge deposition on biodiversity

Chemical Properties, Environmental Fate, and Degradation of Seven Classes of Pollutants

Manzetti, Sergio; van der Spoel, E. Roos; van der Spoel, David

Ingår i Chemical Research in Toxicology, s. 713-737, 2014

• DOI för Chemical Properties, Environmental Fate, and Degradation of Seven Classes of Pollutants

Fullerenes toxicity and electronic properties

Manzetti, Sergio; Behzadi, Hadi; Otto, Andersen; van der Spoel, David

Ingår i Environmental Chemistry Letters, s. 105-118, 2013

• DOI för Fullerenes toxicity and electronic properties

Structural studies of melting on the picosecond time scale

van der Spoel, David; Maia, Filipe R. N. C.; Caleman, Carl

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 6344-6349, 2008

• DOI för Structural studies of melting on the picosecond time scale

Protein Folding Properties from Molecular Dynamics Simulations

Van Der Spoel, David; Patriksson, Alexandra; Seibert, Marvin

Ingår i Applied Parallel Computing, s. 109-115, 2007

Ultrafast Structural Studies on Biological Molecules by X-Rays.

Hajdu, J.; Neutze, R; Wouts, R; van der Spoel, D

Ingår i AIP Conference proceedings, s. 377-385, 1999

Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins

Ghahremanpour, Mohammad Mehdi; van Maaren, Paul J.; Van der Spoel, David

Nanocrystal imaging using intense and ultrashort X-ray pulses

Caleman, Carl; Huldt, Gösta; Ortiz, Carlos; Maia, Filipe R. N. C. et al.

• Ladda ner fulltext (pdf) av Nanocrystal imaging using intense and ultrashort X-ray pulses

Systematic Increase of Force Field Accuracy using the Alexandria Chemistry Toolkit

Nordman, Alfred T.; Rosenbaum, Måns K.; van der Spoel, David

Tripeptide amides that block viral infectivity and methods of use thereof

van der Spoel, David; Hetényi, Csaba; Végvári, Ákos; Höglund, Stefan et al.

2003

Pentamer peptide amide, ALGPGNH2, which inhibits viral infectivity and methods of use thereof

van der Spoel, David; Hetényi, Csaba; Végvári, Ákos; Höglund, Stefan et al.

2003

Pentamer peptide amide, ALGPG-NH2, that inhibits viral infectivity and methods of use thereof

van der Spoel, David; Hetényi, Csaba; Végvári, Ákos; Höglund, Stefan et al.

2002

Structural studies on single particles and biomolecules. LCLS: The First Experiments.

Hajdu, J; Hodgson, K; Miao, J; van der Spoel, D et al.

2000