Department of Cell and Molecular Biology

Publications

Submitted

132. Mónika Bálint, Norbert Jeszenöi, István Horváth, David van der Spoel and Csaba Hetényi: Systematic exploration of multiple drug binding sites Submitted 0 pp. 0 (0)

131. Amanda Tas, Elin Götmark, Stig-Olof Holm and David van der Spoel: Comment on: 'Climate change effects of forestry and substitution of carbon-intensive materials and fossil fuels' Submitted 0 pp. 0 (0)

130. Haiyang Zhang, Yang Jiang, Hai Yan, Chunhua Yin, Tianwei Tan, and David van der Spoel: Free Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton Submitted 0 pp. 0 (0)


2017

129. Jin Zhang, Haiyang Zhang, Tao Wu, Qi Wang and David van der Spoel: Comparison of Implicit and Explicit Solvent Models for the Calculation of Solvation Free Energy in Organic Solvents J. Chem. Theory Comput. 0 pp. 0 (2017) get a copy


2016

128. Haiyang Zhang, Chunhua Yin, Hai Yan and David van der Spoel: Evaluation of Generalized Born Models for Large Scale Affinity Prediction of Cyclodextrin Host−Guest Complexes J. Chem. Inf. Model. 56 pp. 2080-2092 (2016) get a copy

127. Ahmet Yildirim, Jin Zhang, Sergio Manzetti and David van der Spoel: Binding of Pollutants to Biomolecules - A Simulation Study Chem. Res. Toxicol. 29 pp. 1679-1688 (2016) get a copy

126. Mohammad Ghahremanpour and Paul van Maaren and Jonas Ditz and Roland Lindh and David van der Spoel: Large-Scale Calculations of Gas Phase Thermochemistry: Enthalpy of Formation, Standard Entropy and Heat Capacity J. Chem. Phys. 145 pp. 114305 (2016) get a copy

125. Marie-Claire Bellissent-Funel, Ali Hassanali, Martina Havenith, Richard Henchman, Peter Pohl, Fabio Sterpone, David van der Spoel, Yao Xu, and Angel E Garcia: Water Determines the Structure and Dynamics of Proteins Chem. Rev. 116 pp. 7673-7697 (2016) get a copy

124. Jin Zhang, Badamkhatan Tuguldur and David van der Spoel: Correction to Force Field Benchmark of Organic Liquids II: Gibbs Energy of Solvation J. Chem. Inf. Model. 56 pp. 819-820 (2016) get a copy

123. Haiyang Zhang, Yongqin Lv, Tianwei Tan and David van der Spoel: Protein Encapsulation in Metal-Organic Frameworks J. Phys. Chem. B 120 pp. 477-484 (2016) get a copy

122. Norbert Jeszenöi, Mónika Bálint, István Horváth, David van der Spoel and Csaba Hetényi: Exploration of Interfacial Hydration Networks of Target-Ligand Complexes J. Chem. Inf. Model. 56 pp. 148-158 (2016) get a copy


2015

119. Jin Zhang, Badamkhatan Tuguldur and David van der Spoel: Force Field Benchmark of Organic Liquids II: Gibbs Energy of Solvation J. Chem. Inf. Model. 55 (6), pp 1192–1201 (2015) get a copy

118. Nina M. Fischer, Paul J. van Maaren, Jonas C. Ditz, Ahmet Yildirim and David van der Spoel: Properties of Organic Liquids when Simulated with Long-Range Lennard-Jones interactions J. Chem. Theory Comput. 11 (7), pp 2938–2944 (2015) get a copy

117. Justin Lemkul, Benoit Roux, David van der Spoel and Alexander MacKerell: Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model J. Comp. Chem. Volume 36, Issue 19
July 15, Pages 1473–1479 (2015) get a copy

116. Norbert Jeszenöi, István Horváth, Mónika Bálint, David van der Spoel and Csaba Hetényi: Mobility-based prediction of hydration structures of protein surfaces Bioinformatics 31 (12): 1959-1965 (2015) get a copy

115. Alexandr Nasedkin, Moreno Marcellini, Tomasz L. Religa, Stefan M. V. Freund, Andreas Menzel, Alan R. Fersht, Per Jemth, David van der Spoel and Jan Davidsson: Deconvoluting protein folding structural ensembles using X-ray scattering, NMR spectroscopy and molecular dynamics simulation PLoS One pp. 1-14 (2015) get a copy

114. Hadi Behzadi, Payman Roonasi, Khatoon Assle taghipour, David van der Spoel and Sergio Manzetti: Relationship between electronic properties and drug activity of seven quinoxaline compounds: A DFT study J. Mol. Struct. 1091 pp. 196–202 (2015)

113. Alexander Björling, Stephan Niebling, Moreno Marcellini, David van der Spoel and Sebastian Westenhoff: Deciphering solution scattering data with experimentally guided MD simulations J. Chem. Theor. Comput. 11 pp. 780-787 (2015) get a copy


2014

112. Bjorn Steen Sæthre, Alex C. Hoffmann and David van der Spoel: Order parameters and algorithmic approaches for detection and demarcation of interfaces in hydrate-fluid and ice-fluid systems J. Chem. Theor. Comput. 10 pp. 5606-5616 (2014) get a copy

111. Sergio Manzetti, Roos van der Spoel and David van der Spoel: Chemical properties, environmental fate and degradation of seven classes of pollutants Chem. Res. Toxicol. 27 pp. 713-737 (2014) get a copy

110. Haiyang Zhang, Tianwei Tan, Csaba Hetényi, Yongqin Lv and David van der Spoel: Cooperative Binding of Cyclodextrin Dimers to Isoflavone Analogs Studied Elucidated by Free Energy Calculations J. Phys. Chem. C 118 pp. 7163-7173 (2014) get a copy

109. Jochen S. Hub, Maarten G. Wolf, Carl Caleman, Paul J. van Maaren, Gerrit Groenhof and David van der Spoel: Thermodynamics of hydronium and hydroxide surface solvation Chem. Sci. 5 pp. 1745-1749 (2014) get a copy

108. Michiel van Lun, Jochen S. Hub, David van der Spoel and Inger Andersson: CO2 and O2 Distribution in Rubisco Suggests the Small Subunit Functions as a CO2 Reservoir J. Amer. Chem. Soc. 136 pp. 3165-3171 (2014) get a copy

107. Sergio Manzetti, Jin Zhang and David van der Spoel: Thiamin function, metabolism, uptake and transport Biochemistry 53 pp. 821-835 (2014) get a copy

106. Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab, Saman Biook Aghazadeh, Jin Zhang and David van der Spoel: MemBuilder: A Web-Based Graphical Interface to Build Heterogeneously Mixed Membrane Bilayers for the GROMACS Biomolecular Simulation Program Bioinformatics 30 pp. 439-441 (2014) get a copy

105. Lundborg, Magnus; Apostolov, Rossen; Spångberg, Daniel; Gärdenäs, Anders; van der Spoel, David; Lindahl, Erik: An Efficient and Extensible Format, Library and API for Binary Trajectory Data from Molecular Simulations J. Comput. Chem. 35 pp. 260-269 (2014) get a copy


2013

104. Florian Zocher, David van der Spoel, Peter Pohl and Jochen S. Hub: Local micro-partition coefficients govern solute permeability of cholesterol-containing membranes Biophysical J. 105 pp. 2760-2770 (2013) get a copy

103. Erik G. Marklund, Anel Mahmutovic, Otto G. Berg, Petter Hammar, David van der Spoel, David Fange and Johan Elf: Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models Proc. Natl. Acad. Sci. U.S.A. 110 pp. 19796-19801 (2013) get a copy

102. Gadzikano Munyuki, Graham E. Jackson, Gerhard A. Venter, Katalin E. Kövér and László Szilágyii, Marina Rautenbach, Barbara M. Spathelf, Bhaswati Bhattacharya and David van der Spoel: β-sheet structures and dimer models of the two major tyrocidines, antimicrobial peptides from Bacillus aneurinolyticus Biochemistry 52 pp. 7798-7806 (2013) get a copy

101. Haiyang Zhang, Tianwei Tan, Csaba Hetényi and David van der Spoel: Quantification of solvent contribution to the stability of non-covalent complexes J. Chem. Theor. Comput. 9 pp. 4542-4551 (2013) get a copy

100. Tuanan da Costa Lourenco, Mariny F. C. Coelh, Teodorico de Castro Ramalho, David van der Spoel, and Luciano T. Costa: Insights on the solubility of CO2 in 1-ethyl-3-methylimidazolium bis(trifluoro)sulphonylimide from the microscopic point of view Environ. Sci. Technol. 47 pp. 7421-7429 (2013) get a copy

99. Grace Mugumbate, Graham E. Jackson, David van der Spoel, Katalin E. Kover and Laszlo Szilagyi: Anopheles gambiae, Anoga-HrTH hormone, free and bound structure - an nuclear magnetic resonance experiment Peptides 41 pp. 94-100 (2013) get a copy

98. Sergio Manzetti, Hadi Behzadi, Otto Andersen and David Van Der Spoel: Fullerenes toxicity and electronic properties Environmental Chemistry Letters 11 pp. 105-118 (2013) get a copy

97. Sander Pronk, Szilard Pall, Roland Schulz, Per Larsson, Par Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl: GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit Bioinformatics 29 pp. 845-854 (2013) get a copy


2012

96. Haiyang Zhang, Tianwei Tan, Wei Feng and David van der Spoel: Molecular Recognition in Different Environments - β-Cyclodextrin Dimer Formation in Organic Solvents J. Phys. Chem. B 116 pp. 12684-12693 (2012) get a copy

95. Hongqian Yang, David M. Good, David van der Spoel and Roman A. Zubarev: Fragmentation of gas-phase tryptic peptide dications. I. Carbonyl charge solvation pattern reveals the origin of fragmentation classes J. Amer. Soc. Mass Spectrom. 23 pp. 1319-1325 (2012) get a copy

94. Daniel S.D. Larsson and David van der Spoel: Screening for the Location of RNA using the Chloride Ion Distribution in Simulations of Virus Capsids J. Chem. Theor. Comput. 8 pp. 2474-2483 (2012) get a copy

93. Jochen S. Hub, Carl Caleman and David van der Spoel: Organic molecules on the surface of water droplets - An energetic perspective Phys. Chem. Chem. Phys. 14 pp. 9537-9545 (2012) get a copy

92. Bjorn Steen Sæthre, David van der Spoel, Alex C. Hoffmann: Free energy of separation of structure II clathrate hydrate in water and a light oil J. Phys. Chem. B 116 pp. 5933-5940 (2012) get a copy

91. Daniel S.D. Larsson, Lars Liljas and David van der Spoel: Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations PLoS Comput. Biol. 8 pp. e1002502 (2012) get a copy

90. Haiyang Zhang, Chunling Ge, David van der Spoel, Wei Feng and Tianwei Tan: Atomic Insight into Structural Change of Beta-Cyclodextrin Caused by Alcohol Co-solvents and Guest Molecules J. Phys. Chem. B. 116 pp. 3880-3889 (2012) get a copy

89. Christian Wennberg, David van der Spoel and Jochen S. Hub: Large influence of cholesterol on solute partitioning into lipid membranes J. Amer. Chem. Soc. 134 pp. 5351-5361 (2012) get a copy

88. David van der Spoel, Paul J. van Maaren and Carl Caleman: GROMACS Molecule & Liquid Database Bioinformatics 28 pp. 752-753 (2012) get a copy

87. Carl Caleman, Paul J. van Maaren, Minyan Hong, Jochen S. Hub, Luciano T. Costa, David van der Spoel: Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Compressibility, Expansion Coefficient and Dielectric Constant J. Chem. Theor. Comput. 8 pp. 61-74 (2012) get a copy


2011

86. Hadi Behzadi, Mohamad Reza Talei, Bavil Olyai, David van der Spoel: Probing 13C chemical shielding tensors in cryptolepine and two bromosubstituted analogs for antiplasmodial activity J. Mol. Model. 17 pp. 3289-3297 (2011) get a copy

85. Malmerberg, Erik; Omran, Ziad; Hub, Jochen; Li, Xuewen; Katona, Gergely; Westenhoff, Sebastian; Johansson, Linda; Andersson, Magnus; Cammarata, Marco; Wulff, Michael; Van der Spoel, David; Davidsson, Jan; Specht, Alexandre ; Neutze, Richard: Iodinated retinal accelerates conformational changes in the photocycle of proteorhodopsin Biophys. J. 101 pp. 1345-1353 (2011) get a copy

84. Daniel Spångberg, Daniel S. D. Larsson and David van der Spoel: Trajectory Next Generation J. Mol. Model 17 pp. 2669-2685 (2011) get a copy

83. Michiel van Lun, David van der Spoel and Inger Andersson: Subunit Interface Dynamics in Hexadecameric Rubisco J. Mol. Biol. 411 pp. 1083-1098 (2011) get a copy

82. David van der Spoel and Berk Hess: GROMACS - The Road Ahead Comput. Molec. Sci. 1 pp. 710-715 (2011) get a copy

81. Carl Caleman, Jochen S. Hub, Paul J. van Maaren and David van der Spoel: Atomistic Simulation of Ion Solvation in Water Explain Surface Preference of Halides Proc. Natl. Acad. Sci. U.S.A. 108 pp. 6838-6842 (2011) get a copy

80. Csaba Hetényi and David van der Spoel: Towards prediction of functional protein pockets using blind docking and pocket search algorithms Protein Science 20 pp. 880-893 (2011) get a copy

79. F. Wang, E. Weckert, B. Ziaja, D. S. D. Larsson and D. van der Spoel: Coherent Diffraction of a Single Virus Particle: The Impact of a Water Layer on the Available Orientational Information Phys. Rev. E 83 pp. 031907 (2011)

78. Grace Mugumbate, Graham E. Jackson and David van der Spoel: Open Conformation Of Adipokinetic Hormone Receptor From The Malaria Mosquito Facilitates Hormone Binding Peptides 32 pp. 553-559 (2011) get a copy

77. Carl Caleman, Gosta Huldt, Carlos Ortiz, Filipe R.N.C. Maia, Fritz Parak, David van der Spoel, Janos Hajdu and Nicusor Timneanu: Nanocrystal imaging using intense and ultrashort X-ray pulses ACS Nano 5 pp. 139-146 (2011) get a copy

76. David van der Spoel, Erik G. Marklund, Daniel S. D. Larsson and Carl Caleman: Proteins, Lipids and Water in the Gas Phase Macromolecular Bioscience 11 pp. 50-59 (2011) get a copy


2010

75. Jochen S. Hub, Bert de Groot and David van der Spoel: g_wham - A free weighted histogram analysis implementation including robust error and autocorrelation estimates J. Chem. Theor. Comp. 6 pp. 3713-3720 (2010) get a copy

74. Filipe R. N. C. Maia, Tomas Ekeberg, David van der Spoel and Janos Hajdu: Hawk: the image reconstruction package for coherent X-ray diffractive imaging J. Appl. Cryst 43 pp. 1535-1539 (2010) get a copy

73. Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655 (2010) get a copy


2009

72. Friemann, Rosmarie; Larsson, Daniel; Wang, Yaofeng; Van der Spoel, David: Molecular Dynamics Simulations of a Membrane Protein-Micelle Complex in vacuo J. Amer. Chem. Soc. 131 pp. 16606-16607 (2009) get a copy

71. Filipe R.N.C. Maia, Tomas Ekeberg, Nicusor Timneanu, David van der Spoel and Janos Hajdu: Structural variability and the incoherent addition of scattered intensities in single-particle diffraction Phys. Rev. E 80 pp. 031905 (2009)

70. Erik Marklund, Daniel Larsson, Alexandra Patriksson, David van der Spoel & Carl Caleman: Structural stability of electrosprayed proteins: temperature and hydration effects Phys. Chem. Chem. Phys. 11 pp. 8069-8078 (2009) get a copy

69. Hadi Behzadi, Mehdi D. Esrafili, Javad Beheshtian, Nasser L. Hadipour and David van der Spoel: A density functional study of 15N chemical shielding tensors in quinolines Chem. Phys. Lett 476 pp. 196-200 (2009) get a copy

68. Graham E. Jackson, Andre N. Mabula, Shane R. Stone, Gurd Gade, Katalin E. Kover, Laszlo Szilagyi and David van der Spoel: Solution Conformations of an Insect Neuropeptide: Crustacean Cardioactive Peptide (CCAP) Peptides Peptides 30 pp. 557-564 (2009) get a copy

67. Yaofeng Wang, Daniel Larsson and David van der Spoel: Encapsulation of Myoglobin in a CTAB micelle - A Simulation Study Biochemistry 48 pp. 1006-1015 (2009) get a copy


2008

66. David van der Spoel, Filipe N. R. C. Maia and Carl Caleman: Structural Studies of Melting on the Picosecond Time Scale Phys. Chem. Chem. Phys. 10 pp. 6344-6349 (2008) get a copy

65. Hadi Behzadi, Mehdi D. Esrafili, David van der Spoel, Nasser L. Hadipour and Gholamabbas Parsafar: A Theoretical Study of Repeating Sequence in HRP II: A Combination of Molecular Dynamics Simulations and 17O Quadrupole Coupling Tensors Biophys. Chem. 137 pp. 76-80 (2008) get a copy

64. Hadi Behzadi, David van der Spoel, Mehdi D. Esrafili, Gholam Abbas Parsafar, Nasser L. Hadipour: Role of spin state on the geometry and nuclear quadrupole resonance parameters in hemin complex Biophys. Chem. 134 pp. 200-206 (2008) get a copy

63. Alexandra Patriksson and David van der Spoel: A temperature calculator for replica exchange molecular dynamics simulations Phys. Chem. Chem. Phys. 10 pp. 2073-2077 (2008) get a copy

62. Berk Hess, Carsten Kutzner, David van der Spoel and Erik Lindahl: GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theor. Comp. 4 pp. 435-447 (2008) get a copy

61. Carl Caleman and David van der Spoel: Picosecond Melting of Ice by an Infrared Laser Pulse - A Simulation Study Angew. Chem. Intl. Ed. 47 pp. 1417-1420 (2008) get a copy

60. Magnus Andersson, Jonathan Vincent, David van der Spoel, Jan Davidsson and Richard Neutze: A Proposed Time-Resolved X-Ray Scattering Approach to Track Local and Global Conformational Changes in Membrane Transport Proteins Structure 16 pp. 21-28 (2008) get a copy


2007

59. Alexandra Patriksson, Chris Adams, Frank Kjeldsen, Roman Zubarev and David van der Spoel: A direct comparison of protein structure in gas and solution phase - the Trp-cage J. Phys. Chem. B 111 pp. 13147-13150 (2007) get a copy

58. David van der Spoel, Alexandra Patriksson and Marvin Seibert: Protein Folding Properties from Molecular Dynamics Simulations Lecture Notes in Computer Science. 4699 pp. 109-115 (2007) get a copy

57. Carl Caleman and David van der Spoel: Evaporation from water droplets containig singly charged ions Phys. Chem. Chem. Phys. 9 pp. 5105-5111 (2007) get a copy

56. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Speeding up parallel GROMACS on high-latency networks J. Comp. Chem 28 pp. 2075-2084 (2007) get a copy

55. Anthony T. Iavarone, Alexandra Patriksson, David van der Spoel and Joel H. Parks: Fluorescence Probe of Trp-cage Protein Conformation in Solution and in Gas Phase J. Am. Chem. Soc. 129 pp. 6726-6735 (2007) get a copy

54. Alexandra Patriksson, Erik Marklund and David van der Spoel: Proteins Structures under Electrospray Conditions Biochemistry 46 pp. 933-945 (2007) get a copy

53. Abraham Szöke, David van der Spoel and Janos Hajdu: Energy Utilization, Catalysis and Evolution - Emergent Properties of Life Current Chemical Biology 1 pp. 53-57 (2007) get a copy


2006

52. Carsten Kutzner, David van der Spoel, Martin Fechner, Erik Lindahl, Udo W. Schmitt, Bert L. de Groot and Helmut Grubmuller: Improved GROMACS scaling on Ethernet switched clusters Lecture Notes in Computer Science. 4192 pp. 404-405 (2006) get a copy

51. Henry Chapman et al.: Femtosecond diffractive imaging with a soft free-electron laser Nature Physics. 2 pp. 839-843 (2006) get a copy

50. Michiel van Lun and David van der Spoel: Computer simulations of Protein Folding Handbook of Theoretical and Computational Nanotechnology, American Science Publishers 6 pp. 47-69 (2006) get a copy

49. Carl Caleman and David van der Spoel: Temperature and Structural Changes in Water Clusters due to Evaporation in Vacuum J. Chem. Phys. 125 pp. 154508 (2006) get a copy

48. Christopher M. Adams, Frank Kjeldsen, Alexandra Patriksson, David van der Spoel, Astrid Gräslund, Evangelos Papadopoulos, and Roman A. Zubarev: Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques Int. J. Mass. Spectrom. 253 pp. 263-273 (2006) get a copy

47. David van der Spoel and M. Marvin Seibert: Protein Folding Kinetics and Thermodynamics from Atomistic Simulations Phys. Rev. Lett. 96 pp. 238102 (2006)

46. David van der Spoel, Erik J. W. Wensink and Alex C. Hoffmann: Lifting a glass from a wet table: a microscopic picture Langmuir 22 pp. 5666-5672 (2006) get a copy

45. David van der Spoel, Paul J. van Maaren, Per Larsson and Nicusor Timneanu: Thermodynamics of hydrogen bonding in hydrophilic and hydrophobic media J. Phys. Chem. B 110 pp. 4393-4398 (2006) get a copy

44. C. Hetényi and D. van der Spoel: Blind docking of drug-sized ligands to proteins up to thousand residues. FEBS Letters 580 pp. 1447-1450 (2006) get a copy

43. Alexandra Patriksson, Christopher Adams, Frank Kjeldsen, Johan Raber, David van der Spoel and Roman A. Zubarev: Prediction of N-Ca Bond Cleavage Frequencies in Electron Capture Dissociation of Trp-cage Dications by Force-field Molecular Dynamics Simulations Int. J. Mass Spectrom. 248 pp. 124-135 (2006) get a copy

42. David van der Spoel and Paul J. van Maaren: The origin of layer structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11 (2006) get a copy


2005

41. Marvin Seibert, Alexandra Patriksson, Berk Hess and David van der Spoel: Reproducible polypeptide folding and structure prediction using molecular dynamics simulations J. Mol. Biol. 354 pp. 173-183 (2005) get a copy

40. David van der Spoel, Erik Lindahl, Berk Hess, Gerrit Groenhof, Alan E. Mark and Herman J. C. Berendsen: GROMACS: Fast, Flexible and Free J. Comp. Chem. 26 pp. 1701-1719 (2005) get a copy

39. K. J. Gaffney et al.: Observation of structural anisotropy and the onset of liquid-like motion during the nonthermal melting of InSb Phys. Rev. Lett. 95 pp. 125701 (2005) get a copy

38. Filipe Maia, Abraham Szöke, Warren DeLano and David van der Spoel: Interactive visualization of electron density slices J. Appl. Cryst. 38 pp. 563-565 (2005) get a copy

37. A. M. Lindenberg at al.: Atomic-Scale Visualization of Inertial Dynamics Science 308 pp. 392-395 (2005) get a copy

36. A. L. Cavalieri et al.: Clocking Femtosecond X Rays Phys. Rev. Lett. 94 pp. 114801 (2005) get a copy


2004

35. Magnus Bergh, Nicusor Timneanu and David van der Spoel: A model for the dynamics of water clusters in an X-ray FEL beam Phys. Rev. E 70 pp. 051904 (2004) get a copy

34. Richard Neutze, Gösta Huldt, Janos Hajdu and David van der Spoel: Potential impact of an X-ray free electron laser on structural biology Radiation Physics and Chemistry 71 pp. 905-916 (2004) get a copy

33. N. Timneanu, C. Caleman, J. Hajdu and D. van der Spoel: Auger Electron Cascades in Water and Ice Chem. Phys. 299 pp. 277-283 (2004) get a copy

32. K. Edman, A. Royant, G. Larsson, F. Jacobsson, T. Taylor, D. van der Spoel, E. M. Landau, E. Pebay-Peyroula, R. Neutze: Deformation of helix C in the low-temperature L-intermediate of bacteriorhodopsin J. Biol. Chem. 279 pp. 2147-2158 (2004) get a copy

31. C. M. Shepherd and D. van der Spoel and H. J. Vogel: Molecular dynamics simulations of peptides from the central domain of smooth muscle caldesmon J. Biomol. Struct. Dynam. 12 pp. 555-565 (2004) get a copy


2003

30. T. A. Link, M. Iwata, J. Bjorkman, D. van der Spoel, A. Stocker, S. Iwata: Molecular modeling of inhibitors at Q(i) and Q(o) sites in cytochrome bc(1) complex CHEMISTRY OF CROP PROTECTION - PROGRESS AND PROSPECTS IN SCIENCE AND REGULATION pp. 110-127 (2003)

29. David van der Spoel and Erik Lindahl: Brute force molecular dynamics simulations of Villin headpiece: Comparison with NMR parameters J. Phys. Chem. B. 117 pp. 11178-11187 (2003) get a copy

28. Erik J.W. Wensink, Alex C. Hoffmann, Paul J. van Maaren and David van der Spoel: Dynamic properties of water/alcohol mixtures studied by computer simulation J. Chem. Phys. 119 pp. 7308-7317 (2003) get a copy

27. Sergio Manzetti, Daniel R. McCulloch, Adrian C. Herington and David van der Spoel: Molecular dynamics of MMP-3, ADAM-9 and ADAM-10 in complex with hypothetical substrates: New implications for catalysis and substrate affinity J. Comp. Aid. Mol. Des. 17 pp. 551-565 (2003) get a copy


2002

26. B. Ziaja, A. Szöke, D. van der Spoel and J. Hajdu: Space-time evolution of electron cascades in diamond. Phys. Rev. B. 66 pp. 10358 (2002) get a copy

25. C. Hetényi and D. van der Spoel: Efficient docking of peptides to proteins without prior knowledge of the binding site. Prot. Sci. 11 pp. 1729-1737 (2002) get a copy


2001

24. B. Ziaja, D. van der Spoel, A. Szöke and J. Hajdu: Auger electron cascades in diamond and amorphous carbon Phys. Rev. B 64 pp. 214104 (2001) get a copy

23. E. Lindahl, B. Hess and D. vand der Spoel: GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7 pp. 306-317 (2001) get a copy

22. P. J. van Maaren and D. van der Spoel: Molecular Dynamics Simulations of Water With Novel Shell-Model Potentials J. Phys. Chem. B. 105 pp. 2618-2626 (2001) get a copy


2000

21. R. Neutze and R. Wouts and D. van der Spoel and E. Weckert and J. Hajdu: Femtosecond imaging of biomolecules with X-rays Nature 406 pp. 752-757 (2000) get a copy

20. D. P. Tieleman and D. van der Spoel and H. J. C. Berendsen: Molecular Dynamics Simulations of Dodecylphosphocholine Micelles at Three Different Aggregate Sizes: Micellar Structure and Chain Relaxation J. Phys. Chem. B. 104 pp. 6380-6388 (2000) get a copy

19. J. Hajdu and K. Hodgson and J. Miao and D. van der Spoel and R. Neutze and C. V. Robinson and G. Faigel and C. Jacobsen and J. Kirz and D. Sayre and E. Weckert and G. Materlik and A. Szöke: Structural studies on single particles and biomolecules. LCLS: The First Experiments. Published by SSRL, SLAC, Stanford, USA. 0 pp. 35-62 (2000)


1999

18. J. Hajdu and R. Neutze and R. Wouts and D. van der Spoel: Ultrafast Structural Studies on Biological Molecules by X-Rays. AIP Conference proceedings 477 pp. 377-385 (1999)


1998

17. D. van der Spoel: The Solution Conformation of Amino Acids from Molecular Dynamics Simulations of Gly-X-Gly Peptides: Comparison with NMR Parameters Biochem Cell Biol 76 pp. 164-170 (1998) get a copy

16. David van der Spoel, Paul J. van Maaren and Herman J.C. Berendsen: A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field. J Chem Phys 108 pp. 10220-10230 (1998) get a copy

15. David van der Spoel, Aldert R. van Buuren, Emile Apol, Pieter J. Meulenhoff, D. Peter Tieleman, Alfons L. T. M. Sijbers, Berk Hess, K. Anton Feenstra, Rudi van Drunen and Herman J. C. Berendsen: Gromacs User Manual version 2.0, 0 pp. 0 Nij-enborgh 4, 9747 AG Groningen, The Netherlands. (1998) get a copy


1997

14. D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997)

13. F. P. X. Everdij, D. A Wiersma, D. van der Spoel and J. Mavri: Molecular Dynamics Simulation Study of the Photodissociation of the Iodine-Benzene Charge-Transfer Complex Proceedings of the Nobel symposium 101: Femtochemistry and Femtobiology: Ultrafast Reaction Dynamics at Atomic-Scale Resolution 0 pp. 0 Imperial College Press, Sweden (1997)


1996

12. D. van der Spoel: Structure and dynamics of peptides: theoretical aspects of protein folding, PhD Thesis, Univ. of Groningen, 1996. 0 pp. 0 Some paper copies left as well. E-mail me if you want one (1996) get a copy

11. D. van der Spoel, H.J. Vogel and H.J.C. Berendsen: Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein Proteins 24 pp. 450-466 (1996) get a copy

10. D. van der Spoel, B.L. de Groot, S. Hayward, H.J.C. Berendsen and H.J. Vogel: Bending of the calmodulin central helix: a theoretical study Protein Science 5 pp. 2044-2053 (1996) get a copy

9. D. van der Spoel, A.R. van Buuren, D.P. Tieleman and H.J.C. Berendsen: Molecular dynamics simulations of peptides from BPTI: A closer look at amide-aromatic interactions J. Biomol. NMR 8 pp. 229-238 (1996) get a copy

8. D. van der Spoel, K.A. Feenstra, M.A. Hemminga and H.J.C. Berendsen: Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions Biophys. J. 71 pp. 2920-2932 (1996) get a copy

7. N.A.J. van Nuland, J.A. Wiersma, D. van der Spoel, B.L. de Groot, R.M. Scheek and G.T. Robillard: Phosphorylation-induced torsion-angle strain in the active center of HPr, detected by NMR and restrained molecular dynamics refinement Protein Science 5 pp. 442-446 (1996) get a copy


1995

6. D. van der Spoel and H.J.C. Berendsen: Determination of proton transfer rate constants using ab initio, molecular dynamics and density matrix evolution calculations in "Pacific Symposium of Bio-Computing" 0 pp. 624-637 "World Scientific Singapore" (1995)

5. H.J.C. Berendsen, D. van der Spoel and R. van Drunen: GROMACS: A message-passing parallel molecular dynamics implementation Comp. Phys. Comm. 91 pp. 43-56 (1995)

4. P.C. Jordan, P.J. van Maaren, J. Mavri, D. van der Spoel and H.J.C. Berendsen: Towards phase transferable potential functions: Methodology and application to nitrogen J. Chem. Phys. 103 pp. 2272-2285 (1995) get a copy

3. D. van der Spoel and H.J.C. Berendsen: MD Simulation, Section 6.5 in Aspects of computational science, A.J. van der Steen, ed. 0 pp. 367-378 Stichting Nationale Computer Fac., 's-Gravenhage, ISBN 90-70608-33-2 (1995)


1993

2. H. Bekker, H. J. C. Berendsen, E. J. Dijkstra, S. Achterop, R. van Drunen, D. van der Spoel, A. Sijbers, H. Keegstra, B. Reitsma and M. K. R. Renardus: Gromacs Method of Virial Calculation Using a Single Sum Physics Computing 92 pp. 257-261 World Scientific, Singapore (1993)

1. H. Bekker, H. J. C. Berendsen, E. J. Dijkstra, S. Achterop, R. van Drunen, D. van der Spoel, A. Sijbers, H. Keegstra, B. Reitsma and M. K. R. Renardus: Gromacs: A Parallel Computer for Molecular Dynamics Simulations Physics Computing 92 pp. 252-256 World Scientific, Singapore (1993)