David Van der Spoel
Professor at Institutionen för cell- och molekylärbiologi; Beräkningsbiologi och bioinformatik
- Telephone:
- +46 18 471 42 05
- Fax:
- +46 18 51 17 55
- E-mail:
- David.VanderSpoel@icm.uu.se
- Visiting address:
- Husargatan 3
752 37 Uppsala - Postal address:
- Box 596
751 24 UPPSALA
Deputy Director at Institutionen för informationsteknologi; UPPMAX, Uppsala Multidisciplinary Centre for Advanced Computational Science
- E-mail:
- david.vanderspoel@uppmax.uu.se
- Visiting address:
- Hus 10, Lägerhyddsvägen 1
- Postal address:
- Box 337
751 05 Uppsala
- CV:
- Download CV
- ORCID:
- 0000-0002-7659-8526
More information is available to staff who log in.
Keywords
- alexandria
- computational chemistry
- environmental pollutants
- force field
- gromacs
- machine learning
- molecular dynamics
Publications
Recent publications
- Martini on the Rocks (2024)
- Simulations of Amyloid-Forming Peptides in the Crystal State (2023)
- Can molecular dynamics be used to simulate biomolecular recognition? (2023)
- Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations (2023)
- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design (2022)
All publications
Articles
- Martini on the Rocks (2024)
- Simulations of Amyloid-Forming Peptides in the Crystal State (2023)
- Can molecular dynamics be used to simulate biomolecular recognition? (2023)
- Probing Phase Transitions in Organic Crystals Using Atomistic MD Simulations (2023)
- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design (2022)
- Quantitative predictions from molecular simulations using explicit or implicit interactions (2022)
- The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view (2021)
- Classical molecular dynamics (2021)
- Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches (2021)
- Editorial overview (2021)
- NMR Refinement and Peptide Folding Using the GROMACS Software (2021)
- Systematic design of biomolecular force fields (2021)
- Microscopic origins of conductivity in molten salts unraveled by computer simulations (2021)
- Making Soup (2020)
- Theoretical Infrared Spectra (2020)
- An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra (2020)
- Toward a Computational Ecotoxicity Assay (2020)
- A potential for molecular simulation of compounds with linear moieties (2020)
- Propagation of uncertainty in physicochemical data to force field predictions (2020)
- Rotational and Translational Diffusion of Proteins as a Function of Concentration (2019)
- Ten simple rules on how to create open access and reproducible molecular simulations of biological systems (2019)
- Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods (2019)
- Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics (2019)
- Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts (2019)
- Systematically improved melting point prediction (2019)
- Role of Host-Guest Charge Transfer in Cyclodextrin Complexation (2019)
- Impact of Dispersion Coefficient on Simulations of Proteins and Organic Liquids (2018)
- Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations (2018)
- The Alexandria library, a quantum-chemical database of molecular properties for force field development (2018)
- Polarizable Drude Model with s‑Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields (2018)
- Transient isomers in the photodissociation of bromoiodomethane (2018)
- Small Molecule Thermochemistry (2018)
- Phase-Transferable Force Field for Alkali Halides (2018)
- Statistical efficiency of methods for computing free energy of hydration (2018)
- Force Field Benchmark of Amino Acids (2018)
- Systematic exploration of multiple drug binding sites (2017)
- Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations (2017)
- Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1 (2017)
- Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton (2017)
- Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents (2017)
- Water Determines the Structure and Dynamics of Proteins (2016)
- Large-scale calculations of gas phase thermochemistry (2016)
- Large-scale calculations of gas phase thermochemistry: Enthalpy of formation, standard entropy, and heat capacity (2016)
- Exploration of Interfacial Hydration Networks of Target Ligand Complexes (2016)
- Binding of Pollutants to Biomolecules (2016)
- Atomistic Simulation of Protein Encapsulation in Metal-Organic Frameworks (2016)
- Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host-Guest Complexes (2016)
- Relationship between electronic properties and drug activity of seven quinoxaline compounds (2015)
- Deciphering Solution Scattering Data with Experimentally Guided Molecular Dynamics Simulations (2015)
- Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones Interactions (2015)
- Mobility-based prediction of hydration structures of protein surfaces (2015)
- Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model (2015)
- Impact of sludge deposition on biodiversity (2015)
- Deconvoluting Protein (Un)folding Structural Ensembles Using X-Ray Scattering, Nuclear Magnetic Resonance Spectroscopy and Molecular Dynamics Simulation (2015)
- Generalized Born and Explicit Solvent Models for Free Energy Calculations in Organic Solvents (2015)
- Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation (2015)
- MemBuilder (2014)
- Thermodynamics of hydronium and hydroxide surface solvation (2014)
- An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations (2014)
- Chemical Properties, Environmental Fate, and Degradation of Seven Classes of Pollutants (2014)
- Thiamin Function, Metabolism, Uptake, and Transport (2014)
- Order Parameters and Algorithmic Approaches for Detection and Demarcation of Interfaces in Hydrate-Fluid and Ice-Fluid Systems (2014)
- CO2 and O-2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir (2014)
- Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogues Elucidated by Free Energy Calculations (2014)
- Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View (2013)
- Fullerenes toxicity and electronic properties (2013)
- Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models (2013)
- Anopheles gambiae, Anoga-HrTH hormone, free and bound structure (2013)
- beta-Sheet Structures and Dimer Models of the Two Major Tyrocidines, Antimicrobial Peptides from Bacillus aneurinolyticus (2013)
- GROMACS 4.5 (2013)
- Unexpected Effects of Cholesterol on Membrane Permeability (2013)
- Quantification of Solvent Contribution to the Stability of Noncovalent Complexes (2013)
- Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes (2013)
- Force Field Benchmark of Organic Liquids (2012)
- Organic molecules on the surface of water droplets (2012)
- Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations (2012)
- Screening for the Location of RNA Using the Chloride Ion Distribution in Simulations of Virus Capsids (2012)
- Free Energy of Separation of Structure II Clathrate Hydrate in Water and a Light Oil (2012)
- GROMACS molecule & liquid database (2012)
- Large Influence of Cholesterol on Solute Partitioning into Lipid Membranes (2012)
- Carbonyl Charge Solvation Patterns May Relate to Fragmentation Classes in Collision-Activated Dissociation (2012)
- Molecular recognition in different environments (2012)
- Insight into the Structural Deformations of Beta-Cyclodextrin Caused by Alcohol Cosolvents and Guest Molecules (2012)
- Probing (13)C chemical shielding tensors in cryptolepine and two bromo-substituted analogs for antiplasmodial activity (2011)
- Atomistic simulation of ion solvation in water explains surface preference of halides (2011)
- On the Feasibility of Nanocrystal Imaging Using Intense and Ultrashort X-ray Pulses (2011)
- Toward prediction of functional protein pockets using blind docking and pocket search algorithms (2011)
- Time-Resolved WAXS Reveals Accelerated Conformational Changes in Iodoretinal-Substituted Proteorhodopsin (2011)
- Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding (2011)
- Trajectory NG (2011)
- GROMACS (2011)
- Proteins, Lipids, and Water in the Gas Phase (2011)
- Subunit Interface Dynamics in Hexadecameric Rubisco (2011)
- Coherent Diffraction of a Single Virus Particle (2011)
- g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates (2010)
- Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data (2010)
- Hawk (2010)
- A density functional study of N-15 chemical shielding tensors in quinolines (2009)
- Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in Vacuo (2009)
- Solution conformations of an insect neuropeptide (2009)
- Structural variability and the incoherent addition of scattered intensities in single-particle diffraction (2009)
- Structural stability of electrosprayed proteins (2009)
- Encapsulation of myoglobin in a cetyl trimethylammonium bromide micelle in vacuo (2009)
- A proposed time-resolved X-ray scattering approach to track local and global conformational changes in membrane transport proteins (2008)
- A theoretical study of repeating sequence in HRP II (2008)
- Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex (2008)
- Picosecond Melting of Ice by an Infrared Laser Pulse (2008)
- GROMACS 4 (2008)
- A temperature predictor for parallel tempering simulations (2008)
- Structural studies of melting on the picosecond time scale (2008)
- Evaporation from water clusters containing singly charged ions (2007)
- Fluorescence probe of Trp-cage protein conformation in solution and in gas phase (2007)
- Speeding up parallel GROMACS on high-latency networks (2007)
- A direct comparison of protein structure in the gas and solution phase - the Trp-cage (2007)
- Proteins structures under electrospray conditions (2007)
- Energy Utilization, Catalysis and Evolution - Emergent Properties of Life (2007)
- Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques (2006)
- Femtosecond diffractive imaging with a soft-X-ray free-electron laser (2006)
- Blind docking of drug-sized compounds to proteins with up to a thousand residues. (2006)
- Prediction of N-Ca Bond Cleavage Frequencies in Electron Capture Dissociation of Trp-cage Dications by Force-field Molecular Dynamics Simulations (2006)
- Protein folding kinetics and thermodynamics from atomistic simulations (2006)
- The origin of layer structure artifacts in simulations of liquid water (2006)
- Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media. (2006)
- Clocking femtosecond X rays. (2005)
- Observation of structural anisotropy and the onset of liquidlike motion during the nonthermal melting of InSb. (2005)
- Atomic-scale visualization of inertial dynamics. (2005)
- Interactive visualization of electron density slices (2005)
- Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. (2005)
- GROMACS (2005)
- Model for the Dynamics of a Water Cluster in an X-ray Free Electron Laser Beam (2004)
- Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon (2004)
- Auger electron cascades in water and ice (2004)
- Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in complex with hypothetical substrates (2003)
- Dynamic properties of water/alcohol mixtures studied by computer simulation (2003)
- Efficient docking of peptides to proteins without prior knowledge of the binding site (2002)
- Space-time evolution of electron cascades in diamond (2002)
- GROMACS 3.0: a package for molecular simulation and trajectory analysis (2001)
- Molecular dynamics simulations of water with novel shell-model potentials (2001)
- Potential for biomolecular imaging with femtosecond X-ray pulses (2000)
- Molecular dynamics simulations of dodecylphosphocholine micelles at three different aggregate sizes: Micellar structure and chain relaxation (2000)
- The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters (1998)
- Nanocrystal imaging using intense and ultrashort X-ray pulses
- Efficient Physics-Based Polarizable Charges: from Organic Compounds to Proteins
Conferences
- Protein Folding Properties from Molecular Dynamics Simulations (2007)
- Ultrafast Structural Studies on Biological Molecules by X-Rays. (1999)
Patents
- Pentamer peptide amide, ALGPGNH2, which inhibits viral infectivity and methods of use thereof (2003)
- Tripeptide amides that block viral infectivity and methods of use thereof (2003)
- Pentamer peptide amide, ALGPG-NH2, that inhibits viral infectivity and methods of use thereof (2002)
Other
