van der Spoel labb

Min grupp arbetar på att förbättra modeller och metoder för att göra molekyldynamik (MD) simuleringar. Med MD simulering som baseras på en fysikalisk modell kan man studera hur molekyler interagerar och hur de rör sig i tiden. Resultaten kan analyseras för att ta fram grundläggande information om molekyler, vätskor och komplexa biologiska system såsom hela viruspartiklar. Vi studerar viruspartiklar i syfte att förstå infektion: vad händer när en viruspartikel kommer in i en cell? Hur kommer RNA:t ut ur kapsiden? Ett annat ämne vi arbetar på är att förstå hur RNA-genomet kan veckas inuti en liten viruspartikel. Slutligen forskar vi på hur nybyggda virus kan ta sig ut ur en cell igen.

Populärvetenskaplig presentation

Forskargruppen som leds av David van der Spoel fokuserar på att utveckla nya kraftfält för molekylsimuleringar. Forskningsfältet kring simulering av biomolekyler har växt oerhört, delvis på grund av snabbare datorer, men minst lika viktigt har varit att det mjukvarorna har förbättrats kraftigt. Till exempel har Van der Spoel varit med och utvecklat det nu populära paketet GROMACS (https://www.gromacs.org) från början. Dessvärre har kvaliteten på förutsägelserna inte blivit så mycket bättre som de kunde. Gruppen håller därför på att utveckla en ny mjukvara för maskinlärning av kraftfält, som heter Alexandria Chemistry Toolkit, och som snart kommer att släppas här: https://github.com/AlexandriaChemistry. Med denna mjukvara går det att evaluera kraftfält steg för steg och på så sätt går det att höja noggrannheten i förutsägelserna systematiskt.

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
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?
- Ladda ner fulltext (pdf) av Martini on the Rocks: Can a Coarse-Grained Force Field Model Crystals?
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
- Ladda ner fulltext (pdf) av Assessment of Climate Impact of Sustainable Forestry Based on Landscape Structure
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
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
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?
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
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
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
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
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
Classical molecular dynamics

Brooks, Charles L., III; 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
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
- Ladda ner fulltext (pdf) av Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields
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
- Ladda ner fulltext (pdf) av A potential for molecular simulation of compounds with linear moieties
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
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
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
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
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
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
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
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
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
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
- Ladda ner fulltext (pdf) av Ten simple rules on how to create open access and reproducible molecular simulations of biological systems
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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.

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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)

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