Publications

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

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

Part of International Journal of Molecular Sciences, 2022.

DOI for Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design Download full text (pdf) of Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design

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

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

Part of Communications Chemistry, 2021.

DOI for Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches Download full text (pdf) of Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

Classical molecular dynamics

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

Part of Journal of Chemical Physics, 2021.

DOI for Classical molecular dynamics

Editorial overview: Theory and simulation and their new friends

Shehu, Amarda; Van der Spoel, David

Part of Current opinion in structural biology, p. III-V, 2021.

DOI for Editorial overview: Theory and simulation and their new friends

Microscopic origins of conductivity in molten salts unraveled by computer simulations

Walz, Marie-Madeleine; Van der Spoel, David

Part of Communications Chemistry, 2021.

DOI for Microscopic origins of conductivity in molten salts unraveled by computer simulations Download full text (pdf) of Microscopic origins of conductivity in molten salts unraveled by computer simulations

NMR Refinement and Peptide Folding Using the GROMACS Software

Sinelnikova, Anna; Van der Spoel, David

Part of Journal of Biomolecular NMR, p. 143-149, 2021.

DOI for NMR Refinement and Peptide Folding Using the GROMACS Software Download full text (pdf) of 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.

Part of Journal of Chemical Physics, 2021.

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

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.

Part of Journal of Chemical Physics, 2020.

DOI for A potential for molecular simulation of compounds with linear moieties Download full text (pdf) of A potential for molecular simulation of compounds with linear moieties

An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

Henschel, Henning; Van der Spoel, David

Part of Journal of Physical Chemistry Letters, p. 5471-5475, 2020.

DOI for An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra Download full text (pdf) of An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

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

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

Part of Journal of Chemical Information and Modeling, p. 322-331, 2020.

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

Propagation of uncertainty in physicochemical data to force field predictions

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

Part of Physical Review Research, 2020.

DOI for Propagation of uncertainty in physicochemical data to force field predictions Download full text (pdf) of Propagation of uncertainty in physicochemical data to force field predictions

Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

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

Part of Journal of Chemical Theory and Computation, p. 3307-3315, 2020.

DOI for Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields Download full text (pdf) of Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

Toward a Computational Ecotoxicity Assay

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

Part of Journal of Chemical Information and Modeling, p. 3792-3803, 2020.

DOI for Toward a Computational Ecotoxicity Assay

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

Walz, Marie-Madeleine; Van der Spoel, David

Part of The Journal of Physical Chemistry C, p. 25596-25602, 2019.

DOI for 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

Part of Physical Chemistry, Chemical Physics - PCCP, p. 18516-18524, 2019.

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

Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

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

Part of ACS Omega, p. 13772-13781, 2019.

DOI for Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods Download full text (pdf) of Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

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

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

Part of The Journal of Physical Chemistry C, p. 17745-17756, 2019.

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

Rotational and Translational Diffusion of Proteins as a Function of Concentration

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

Part of ACS Omega, p. 20654-20664, 2019.

DOI for Rotational and Translational Diffusion of Proteins as a Function of Concentration Download full text (pdf) of Rotational and Translational Diffusion of Proteins as a Function of Concentration

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

Walz, Marie-Madeleine; Van der Spoel, David

Part of Chemical Communications, p. 12044-12047, 2019.

DOI for Systematically improved melting point prediction: a detailed physical simulation model is required Download full text (pdf) of Systematically improved melting point prediction: a detailed physical simulation model is required

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.

Part of PloS Computational Biology, 2019.

DOI for Ten simple rules on how to create open access and reproducible molecular simulations of biological systems Download full text (pdf) of Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

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

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

Part of Journal of Chemical Information and Modeling, p. 1037-1052, 2018.

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

Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

Bashardanesh, Zahedeh; van der Spoel, David

Part of Journal of Physical Chemistry B, p. 8018-8027, 2018.

DOI for Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids

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

Part of Nucleic Acids Research, p. 4872-4882, 2018.

DOI for Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations Download full text (pdf) of Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations

Phase-Transferable Force Field for Alkali Halides

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

Part of Journal of Chemical Theory and Computation, p. 5933-5948, 2018.

DOI for Phase-Transferable Force Field for Alkali Halides

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.

Part of Journal of Chemical Theory and Computation, p. 5553-5566, 2018.

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

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

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

Part of Journal of Physical Chemistry A, p. 8982-8988, 2018.

DOI for 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

Part of Journal of Chemical Physics, 2018.

DOI for Statistical efficiency of methods for computing free energy of hydration Download full text (pdf) of Statistical efficiency of methods for computing free energy of hydration

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

Part of Scientific Data, 2018.

DOI for The Alexandria library, a quantum-chemical database of molecular properties for force field development Download full text (pdf) of The Alexandria library, a quantum-chemical database of molecular properties for force field development

Transient isomers in the photodissociation of bromoiodomethane

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

Part of Journal of Chemical Physics, 2018.

DOI for Transient isomers in the photodissociation of bromoiodomethane

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.

Part of Journal of Chemical Theory and Computation, p. 1034-1043, 2017.

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

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.

Part of Journal of Physical Chemistry Letters, p. 2705-2712, 2017.

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

Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

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

Part of Molecular Cell, p. 847-859.e7, 2017.

DOI for Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1 Download full text (pdf) of Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

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

Part of Journal of Physics, 2017.

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

Systematic exploration of multiple drug binding sites

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

Part of Journal of Cheminformatics, 2017.

DOI for Systematic exploration of multiple drug binding sites Download full text (pdf) of Systematic exploration of multiple drug binding sites

Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

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

Part of Journal of Physical Chemistry B, p. 477-484, 2016.

DOI for Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks

Binding of Pollutants to Biomolecules: A Simulation Study

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

Part of Chemical Research in Toxicology, p. 1679-1688, 2016.

DOI for Binding of Pollutants to Biomolecules: A Simulation Study Download full text (pdf) of 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

Part of Journal of Chemical Information and Modeling, p. 2080-2092, 2016.

DOI for Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes Download full text (pdf) of 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.

Part of Journal of Chemical Information and Modeling, p. 148-158, 2016.

DOI for 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.

Part of Journal of Chemical Physics, 2016.

DOI for Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity Download full text (pdf) of Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity

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.

Part of Journal of Chemical Physics, 2016.

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

Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

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

Part of Journal of Chemical Theory and Computation, p. 780-787, 2015.

DOI for Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations Download full text (pdf) of Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations

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.

Part of PLOS ONE, 2015.

DOI for Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation Download full text (pdf) of Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation

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

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

Part of JOURNAL OF CHEMICAL INFORMATION AND MODELING, p. 1192-1201, 2015.

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

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

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

Part of Journal of Chemical Theory and Computation, p. 5103-5113, 2015.

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

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., Jr.

Part of Journal of Computational Chemistry, p. 1473-1479, 2015.

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

Mobility-based prediction of hydration structures of protein surfaces

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

Part of Bioinformatics, p. 1959-1965, 2015.

DOI for Mobility-based prediction of hydration structures of protein surfaces

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.

Part of Journal of Chemical Theory and Computation, p. 2938-2944, 2015.

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

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.

Part of Journal of Molecular Structure, p. 196-202, 2015.

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

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.

Part of Journal of Computational Chemistry, p. 260-269, 2014.

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

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

Part of Journal of the American Chemical Society, p. 3165-3171, 2014.

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

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

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

Part of The Journal of Physical Chemistry C, p. 7163-7173, 2014.

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

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.

Part of Bioinformatics, p. 439-441, 2014.

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

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

Part of Journal of Chemical Theory and Computation, p. 5606-5615, 2014.

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

Thermodynamics of hydronium and hydroxide surface solvation

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

Part of Chemical Science, p. 1745-1749, 2014.

DOI for Thermodynamics of hydronium and hydroxide surface solvation

Thiamin Function, Metabolism, Uptake, and Transport

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

Part of Biochemistry, p. 821-835, 2014.

DOI for Thiamin Function, Metabolism, Uptake, and Transport

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.

Part of Peptides, p. 94-100, 2013.

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

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.

Part of Biochemistry, p. 7798-7806, 2013.

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

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

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

Part of Bioinformatics, p. 845-854, 2013.

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

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.

Part of Environmental Science and Technology, p. 7421-7429, 2013.

DOI for 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.

Part of Biophysical Journal, p. 2760-2770, 2013.

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

Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

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

Part of Journal of Chemical Theory and Computation, p. 4542-4551, 2013.

DOI for Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

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.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 19796-19801, 2013.

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

Unexpected Effects of Cholesterol on Membrane Permeability

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

Part of Biophysical Journal, p. 192A-193A, 2013.

DOI for Unexpected Effects of Cholesterol on Membrane Permeability

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.

Part of Journal of the American Society for Mass Spectrometry, p. 1319-1325, 2012.

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

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.

Part of Journal of Chemical Theory and Computation, p. 61-74, 2012.

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

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.

Part of Journal of Physical Chemistry B, p. 5933-5940, 2012.

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

GROMACS molecule & liquid database

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

Part of Bioinformatics, p. 752-753, 2012.

DOI for GROMACS molecule & liquid database

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.

Part of Journal of Physical Chemistry B, p. 3880-3889, 2012.

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

Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes

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

Part of Journal of the American Chemical Society, p. 5351-5361, 2012.

DOI for 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

Part of Journal of Physical Chemistry B, p. 12684-12693, 2012.

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

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

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

Part of Physical Chemistry, Chemical Physics - PCCP, p. 9537-9545, 2012.

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

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

Larsson, Daniel; van der Spoel, David

Part of Journal of Chemical Theory and Computation, p. 2474-2483, 2012.

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

Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

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

Part of PloS Computational Biology, p. e1002502-, 2012.

DOI for Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations Download full text (pdf) of Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations

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

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 6838-6842, 2011.

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

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.

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, p. 031907-1-031907-5, 2011.

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

GROMACS: the road ahead

van der Spoel, David; Hess, Berk

Part of Wiley Interdisciplinary Reviews: Computational Molecular Science, p. 710-715, 2011.

DOI for GROMACS: the road ahead

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.

Part of ACS Nano, p. 139-146, 2011.

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

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

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

Part of Peptides, p. 553-559, 2011.

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

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

Part of Journal of Molecular Modeling, p. 3289-3297, 2011.

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

Proteins, Lipids, and Water in the Gas Phase

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

Part of Macromolecular Bioscience, p. 50-59, 2011.

DOI for Proteins, Lipids, and Water in the Gas Phase

Subunit Interface Dynamics in Hexadecameric Rubisco

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

Part of Journal of Molecular Biology, p. 1083-1098, 2011.

DOI for Subunit Interface Dynamics in Hexadecameric Rubisco

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

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

Part of Biophysical Journal, p. 1345-1353, 2011.

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

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

Hetenyi, Csaba; van der Spoel, David

Part of Protein Science, p. 880-893, 2011.

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

Trajectory NG: portable, compressed, general molecular dynamics trajectories

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

Part of Journal of Molecular Modeling, p. 2669-2685, 2011.

DOI for Trajectory NG: portable, compressed, general molecular dynamics trajectories

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

Part of Journal of Chemical Theory and Computation, p. 3713-3720, 2010.

DOI for 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

Part of Journal of applied crystallography, p. 1535-1539, 2010.

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

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

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

Part of Biophysical Journal, p. 647-655, 2010.

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

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

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

Part of Chemical Physics Letters, p. 196-200, 2009.

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

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

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

Part of Biochemistry, p. 1006-1015, 2009.

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

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

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

Part of Journal of the American Chemical Society, p. 16606-16607, 2009.

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

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

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

Part of Peptides, p. 557-564, 2009.

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

Structural stability of electrosprayed proteins: temperature and hydration effects

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

Part of Physical Chemistry, Chemical Physics - PCCP, p. 8069-8078, 2009.

DOI for Structural stability of electrosprayed proteins: temperature and hydration effects

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.

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, p. 031905-, 2009.

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

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.

Part of Structure, p. 21-28, 2008.

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

A temperature predictor for parallel tempering simulations

Patriksson, Alexandra; van der Spoel, David

Part of Physical Chemistry, Chemical Physics - PCCP, p. 2073-2077, 2008.

DOI for A temperature predictor for parallel tempering simulations

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.

Part of Biophysical Chemistry, p. 76-80, 2008.

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

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

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

Part of Journal of Chemical Theory and Computation, p. 435-447, 2008.

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

Picosecond Melting of Ice by an Infrared Laser Pulse

Caleman, Carl; van der Spoel, David

Part of Angewandte Chemie International Edition, p. 1417-1420, 2008.

DOI for Picosecond Melting of Ice by an Infrared Laser Pulse

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.

Part of Biophysical Chemistry, p. 200-206, 2008.

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

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.

Part of Journal of Physical Chemistry B, p. 13147-13150, 2007.

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

Energy Utilization, Catalysis and Evolution - Emergent Properties of Life

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

Part of Current Chemical Biology, p. 53-57, 2007.

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

Evaporation from water clusters containing singly charged ions

Caleman, Carl; van der Spoel, David

Part of Physical Chemistry, Chemical Physics - PCCP, p. 5105-5111, 2007.

DOI for Evaporation from water clusters containing singly charged ions

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.

Part of Journal of the American Chemical Society, p. 6726-6735, 2007.

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

Proteins structures under electrospray conditions

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

Part of Biochemistry, p. 933-945, 2007.

DOI for Proteins structures under electrospray conditions

Speeding up parallel GROMACS on high-latency networks

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

Part of Journal of Computational Chemistry, p. 2075-2084, 2007.

DOI for Speeding up parallel GROMACS on high-latency networks

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

Hetenyi, Csaba; van der Spoel, David

Part of FEBS Lett, p. 1447-50, 2006.

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

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

Part of Nature Physics, p. 839-843, 2006.

DOI for 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.

Part of Int. J. Mass Spectrom., p. 124-135, 2006.

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.

Part of International Journal of Mass Spectrometry, p. 263-273, 2006.

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

Protein folding kinetics and thermodynamics from atomistic simulations

van der Spoel, David; Seibert, M Marvin

Part of Physical Review Letters, p. 238102-, 2006.

DOI for Protein folding kinetics and thermodynamics from atomistic simulations

The origin of layer structure artifacts in simulations of liquid water

Van Der Spoel, David; van Maaren, Paul

Part of J. Chem. Theor. Comp., p. 1-11, 2006.

Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media.

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

Part of J Phys Chem B, p. 4393-8, 2006.

Atomic-scale visualization of inertial dynamics.

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

Part of Science, p. 392-5, 2005.

Clocking femtosecond X rays.

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

Part of Phys Rev Lett, p. 114801-, 2005.

GROMACS: fast, flexible, and free.

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

Part of J Comput Chem, p. 1701-18, 2005.

Interactive visualization of electron density slices

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

Part of J. Appl. Cryst., p. 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.

Part of Phys Rev Lett, p. 125701-, 2005.

Reproducible polypeptide folding and structure prediction using molecular dynamics simulations.

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

Part of J Mol Biol, p. 173-83, 2005.

Auger electron cascades in water and ice

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

Part of Chemical Physics, p. 277-283, 2004.

DOI for Auger electron cascades in water and ice

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

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

Part of Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, p. 051904-, 2004.

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

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

Part of J. Biomol. Struct. Dynam., p. 555-565, 2004.

Dynamic properties of water/alcohol mixtures studied by computer simulation

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

Part of J. Chem. Phys., p. 7308-7317, 2003.

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

Part of Journal of Computer-Aided Molecular Design, p. 551-565, 2003.

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

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

Hetenyi, C; van der Spoel, D

Part of PROTEIN SCIENCE, p. 1729-1737, 2002.

Space-time evolution of electron cascades in diamond

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

Part of PHYS REV B, 2002.

GROMACS 3.0: a package for molecular simulation and trajectory analysis

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

Part of JOURNAL OF MOLECULAR MODELING, p. 306-317, 2001.

Molecular dynamics simulations of water with novel shell-model potentials

van Maaren, PJ; van der Spoel, D

Part of JOURNAL OF PHYSICAL CHEMISTRY B, p. 2618-2626, 2001.

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

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

Part of JOURNAL OF PHYSICAL CHEMISTRY B, p. 6380-6388, 2000.

Potential for biomolecular imaging with femtosecond X-ray pulses

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

Part of NATURE, p. 752-757, 2000.

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

van der Spoel, D

Part of BIOCHEMISTRY AND CELL BIOLOGY-BIOCHIMIE ET BIOLOGIE CELLULAIRE, p. 164-170, 1998.