Willy Wriggers Publications and Supplementary Data

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Full List of Publications

    2012

  1. Willy Wriggers, Wilma K. Olson and Cristobal G. dos Remedios. Computational Opportunities for Remote Collaboration and Capacity Building afforded by Web 2.0 and Cloud Computing. Biophysical Reviews. Vol. 4. pp. 153-160, 2012. [Abstract] [Editorial] [Article]

  2. Zbigniew Starosolski, Marek Szczepanski, Manuel Wahle, Mirabela Rusu, and Willy Wriggers. Developing a Denoising Filter for Electron Microscopy and Tomography Data in the Cloud. Biophysical Reviews, Vol. 4, pp. 223-229, 2012. [Abstract] [Editorial] [Article] [Suppl. PDF]

  3. Willy Wriggers. Conventions and Work Flows for using Situs. Acta Cryst. D, 2012. Vol. 68, pp. 344-351. [Abstract] [Article] [Suppl. PDF]

  4. Mirabela Rusu, Richard Bonneau, Michael R. Holbrook, Stanley J. Watowich, Stefan Birmanns, Willy Wriggers and Alexander N. Freiberg. An assembly model of Rift Valley fever virus. Frontiers in Microbiology. Vol. 3, Number 00254, 2012. [Abstract] [Article] [Suppl. PDBs]

  5. Mirabela Rusu, Zbigniew Starosolski, Manuel Wahle, Alexander Rigort, and Willy Wriggers. Automated Tracing of Filaments in 3D Electron Tomography Reconstructions using Sculptor and Situs. J. Struct. Biol., Vol. 178, pp. 121-128, 2012. [Abstract] [Article] [SI 1 PDF] [SI 2 ZIP] [SI 3 ZIP] [SI 4 PDF] [SI 5 ZIP] [SI 6 ZIP]

  6. Richard Henderson, Andrej Sali, Matthew L. Baker, Bridget Carragher, Batsal Devkota, Kenneth H. Downing, Edward H. Egelman, Zukang Feng, Joachim Frank, Nikolaus Grigorieff, Wen Jiang, Steven J. Ludtke, Ohad Medalia, Pawel A. Penczek, Peter B. Rosenthal, Michael G. Rossmann, Michael F. Schmid, Gunnar F. Schroder, Alasdair C. Steven, David L. Stokes, John D. Westbrook, Willy Wriggers, Huanwang Yang, Jasmine Young, Helen M. Berman, Wah Chiu, Gerard J. Kleywegt, and Catherine L. Lawson. Outcome of the First Electron Microscopy Validation Task Force Meeting. Structure. 2012, Vol. 20, pp. 205-214. [Abstract] [Article]

  7. Mirabela Rusu, and Willy Wriggers. Evolutionary Bidirectional Expansion for the Tracing of Alpha Helices in Cryo-Electron Microscopy Reconstructions. J. Struct. Biol. 2012, Vol. 177, pp. 410-419. [Abstract] [Article]

    8. 2011

  8. Zhiyong Zhang and Willy Wriggers. Polymorphism of the Epidermal Growth Factor Receptor Extracellular Ligand Binding Domain: The Dimer Interface Depends on Domain Stabilization. Biochemistry, Vol. 50, pp. 2144-2156, 2011. [Abstract] [Article] [Suppl. PDBs]

  9. Willy Wriggers, Lorenzo Alamo, and Raúl Padrón. Matching Structural Densities from Different Biophysical Origins with Gain and Bias. J. Struct. Biol., Vol. 173, pp. 445-450, 2011. [Abstract] [Article]

  10. Stefan Birmanns, Mirabela Rusu, and Willy Wriggers. Using Sculptor and Situs for Simultaneous Assembly of Atomic Components into Low-Resolution Shapes. J. Struct. Biol., Vol. 173, pp. 428–435, 2011. [Abstract] [Article]

    11. 2010

  11. David E. Shaw, Paul Maragakis, Kresten Lindorff-Larsen, Stefano Piana, Ron O. Dror, Michael P. Eastwood, Joseph A. Bank, John M. Jumper, John K. Salmon, Yibing Shan, and Willy Wriggers. Atomic-Level Characterization of the Structural Dynamics of Proteins. Science 2010, Vol. 330, pp. 341-346. [Abstract] [Article] [Suppl. PDF] [Suppl. PDBs] [Science News of the Week] [Runner Up, Science Breakthrough of the Year]

  12. Willy Wriggers. Using Situs for the Integration of Multi-Resolution Structures. Biophysical Reviews 2010, Vol. 2, pp. 21-27. [Abstract] [Article + SI]

    13. 2009

  13. Willy Wriggers, Kate A. Stafford, Yibing Shan, Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, and David E. Shaw. Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2009, Vol. 5, pp. 2595-2605. [Abstract] [Article] [SI] [Original SI Movie Indeo Video 5 Codec AVI] [SI Movie Hi Res Quicktime]

  14. Joseph N. Stember and Willy Wriggers. Bend-Twist-Stretch Model for Coarse Elastic Network Simulation of Biomolecular Motion. J. Chem. Phys. 2009, 131:074112. [Abstract] [Article] [Link]

    15. 2008

  15. Lorenzo Alamo, Willy Wriggers, Antonio Pinto, Fulvia Bártoli, Leiría Salazar, Fa-Qing Zhao, Roger Craig, and Raúl Padrón. Three-Dimensional Reconstruction of Tarantula Myosin Filament Suggests How Phosphorylation May Regulate Myosin Activity. J. Mol. Biol. 2008, Vol. 384, pp. 780-797. [Abstract] [Article] [SI] [SI Movie] [PDB Entry 3DTP] [EMDB Entry 1950]

  16. Zhiyong Zhang and Willy Wriggers. Coarse-Graining Protein Structures With Local Multivariate Features from Molecular Dynamics. J. Phys. Chem. B 2008, Vol. 112, pp. 14026-14035. [Abstract] [Article]

  17. Mirabela Rusu, Stefan Birmanns, and Willy Wriggers. Biomolecular Pleiomorphism Probed by Spatial Interpolation of Coarse Models. Bioinformatics 2008, Vol. 24, pp. 2460-2466. [Abstract] [Article + SI] [Link 1] [Link 2]

    18. 2007

  18. Andreas G. Martin, Frank Depoix, Michael Stohr, Ulrich Meissner, Silke Hagner-Holler, Kada Hammouti, Thorsten Burmester, Jochen Heyd, Willy Wriggers, and Juergen Markl. Limulus polyphemus hemocyanin: 10 A structure, sequence analysis, molecular modelling and rigidbody fitting reveals the interfaces between the eight hexamers. J. Mol. Biol. 2007, Vol. 366, pp. 1332-1350. [Abstract] [Article]
    19.

  19. Stefan Birmanns and Willy Wriggers. Multi-Resolution Anchor-Point Registration of Biomolecular Assemblies and Their Components. J. Struct. Biol. 2007, Vol. 157, pp. 271-280. [Abstract] [Article]
    20.

    2006

  20. Zhiyong Zhang, Paul C. Boyle, Bao-Yuan Lu, Jui-Yoa Chang, and Willy Wriggers. Entropic Folding Pathway of Human Epidermal Growth Factor Explored by Disulfide Scrambling and Amplified Collective Motion Simulations. Biochemistry. 2006, Vol. 45, pp. 15269-15278. [Abstract] [Article]
    21.

  21. Willy Wriggers, Zhiyong Zhang, Mili Shah, and Danny C. Sorensen. Simulating Nanoscale Functional Motions of Biomolecules. Molecular Simulation 2006, Vol. 32, pp. 803-815. [Abstract] [Article]
    22.

  22. Zhiyong Zhang and Willy Wriggers. Local Feature Analysis: A Statistical Theory for Reproducible Essential Dynamics of Large Macromolecules. Proteins: Structure, Function, and Bioinformatics. 2006, Vol. 64, pp. 391-403. [Abstract] [Article]
    23.

    2005

  23. Thomas E. Angelini, Hongjun Liang, Willy Wriggers and Gerard C. L. Wong. Direct observation of counterion organization in F-actin polyelectrolyte bundles. Eur. Phys. J. E, 2005, Vol. 16, pp. 389-400 [Abstract] [Article]

  24. Willy Wriggers, Sugoto Chakravarty, and Patricia A. Jennings. Control of Protein Functional Dynamics by Peptide Linkers. Peptide Science, 2005, Vol. 80, pp. 736-746. [Abstract] [Article]

  25. Oliver Passon, Maik Boltes, Stefan Birmanns, Herwig Zilken, and Willy Wriggers. Laplace-Filter Enhanced Haptic Rendering of Biomolecules. In: Proceedings Vision Modeling and Visualization, G. Greiner, J. Hornegger, H. Niemann, M. Stamminger, Editors, 2005, pp. 311-318 & 516, IOS Press, Netherlands, ISBN 1-58603-569-X. [Abstract] [Reprint]

  26. Yao Cong, Wen Jiang, Stefan Birmanns, Z. Hong Zhou, Wah Chiu, and Willy Wriggers. Fast Rotational Matching of Single Particle Images. J. Struct. Biol., 2005, Vol. 152, pp. 104-112. [Abstract] [Article]

  27. Thomas E. Angelini, Lori K. Sanders, Hongjun Liang, Willy Wriggers, Jay X. Tang and Gerard C. L. Wong. Structure and dynamics of condensed multivalent ions within polyelectrolyte bundles: a combined x-ray diffraction and solid-state NMR study. Journal of Physics: Condensed Matter, 2005, Vol. 17, pp. S1123-S1135 [Abstract] [Article]

    28. 2004

  28. Ryoichi Arai, Willy Wriggers, Yukihiro Nishikawa, Teruyuki Nagamune, and Tetsuro Fujisawa. Conformations of Variably Linked Chimeric Proteins Evaluated by Synchrotron X-ray Small-Angle Scattering. Proteins: Structure, Function, and Bioinformatics, 2004, Vol. 57, pp. 829-238. [Abstract] [Article]

  29. Stefan Birmanns, Maik Boltes, Herwig Zilken, and Willy Wriggers. Adaptive Visuo-Haptic Rendering for Hybrid Modeling of Macromolecular Assemblies. In: Proceedings Mechatronics and Robotics, P. Drews, Editor, 2004, Vol. 4, pp. 1351-1356, Eysoldt Verlag, Germany, ISBN 3-938153-30-X. [Abstract] [Reprint]

  30. Willy Wriggers, Pablo Chacón, Julio Kovacs, Florence Tama and Stefan Birmanns. Topology Representing Neural Networks Reconcile Biomolecular Shape, Structure, and Dynamics. Neurocomputing, 2004, Vol. 56, pp. 365-379. [Abstract] [Article]

  31. Willy Wriggers. Spanning the Length Scales of Biomolecular Simulation. Structure, 2004, Vol. 12, pp. 1-2. [Abstract] [Article] [Previewed Article]

    32. 2003

  32. Stefan Birmanns and Willy Wriggers. Interactive Fitting Augmented by Force-Feedback and Virtual Reality. J. Struct. Biol., 2003, Vol. 144, pp. 123-131. [Abstract] [Article]

  33. Yao Cong, Julio Kovacs, and Willy Wriggers. 2D Fast Rotational Matching for Image Processing of Biophysical Data. J. Struct. Biol., 2003, Vol. 144, pp. 51-60. [Abstract] [Article]

  34. Natacha Opalka, Mark Chlenov, Pablo Chacón, William J. Rice, Willy Wriggers, and Seth Darst. Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase. Cell, 2003, Vol. 114, pp. 335-345. [Abstract] [Article] [Cell Introduction]

  35. Julio A. Kovacs, Pablo Chacón, Yao Cong, Essam Metwally, and Willy Wriggers. Fast Rotational Matching of Rigid Bodies by Fast Fourier Transform Acceleration of Five Degrees of Freedom. Acta Cryst. D, 2003, Vol. 59, pp. 1371-1376. [Abstract] [Article]

  36. Thomas E. Angelini, Hongjun Liang, Willy Wriggers and Gerard Wong. Like-charge attraction between polyelectrolytes induced by counterion charge density waves. PNAS, 2003, Vol. 100, pp. 8634-8637. [Abstract] [Article] [Software]

  37. Pablo Chacón, Florence Tama and Willy Wriggers. Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions. J. Mol. Biol., 2003, Vol. 326, pp. 485-492. [Abstract] [Article]

    38. 2002

  38. Florence Tama, Willy Wriggers, and Charles L. Brooks III. Exploring Global Distortions of Biological Macromolecules and Assemblies from Low-Resolution Structural Information and Elastic Network Theory. J. Mol. Biol., 2002, Vol. 321, pp. 297-305. [Abstract] [Article]

  39. Julio Kovacs and Willy Wriggers. Fast Rotational Matching. Acta Cryst. D, 2002, Vol. 58, pp. 1282-1286. [Abstract] [Article]

  40. Xiaoyi Yao, Vinh Nguyen, Willy Wriggers, and Peter Rubenstein. Regulation of Yeast Actin Behavior by Interaction of Charged Residues Across the Interdomain Cleft. J. Biol. Chem., 2002, Vol. 25, pp. 22875-22882. [Abstract] [Article] [Predicted Structures]

  41. Seth A. Darst, Natacha Opalka, Pablo Chacón, Andrey Polyakov, Catherine Richter, Gongyi Zhang, and Willy Wriggers. Conformational Flexibility of Bacterial RNA Polymerase. PNAS, 2002, Vol. 99, pp. 4296-4301. [Abstract] [Article] [Structure Paper Alert] [Predicted Structure and Movies]

  42. Pablo Chacón and Willy Wriggers. Multi-Resolution Contour-Based Fitting of Macromolecular Structures. J. Mol. Biol., 2002, Vol 317, pp. 375-384. [Abstract] [Article] [Updated Link] [Structure Paper Alert]

    2001

  43. Willy Wriggers and Pablo Chacón. Using Situs for the Registration of Protein Structures with Low-Resolution Bead Models from X-ray Solution Scattering. J. Appl. Cryst., 2001, Vol. 34, pp. 773-776. [Abstract] [Article] [Updated Link]

  44. Willy Wriggers and Pablo Chacón. Modeling Tricks and Fitting Techniques for Multi-Resolution Structures. Structure, 2001, Vol. 9, pp. 779-788. [1st Paragraph] [Article]

  45. Willy Wriggers and Stefan Birmanns. Using Situs for Flexible and Rigid-Body Fitting of Multi-Resolution Single Molecule Data. J. Struct. Biol., 2001, Vol. 133, pp. 193-202. [Abstract] [Article] [Updated Links: 1 2]

  46. Vitold E. Galkin, Albina Orlova, Natalya Lukoyanova, Willy Wriggers, and Edward H. Egelman. ADF Stabilizes an Existing State of F-actin and Can Change the Tilt of F-actin Subunits. J. Cell Biol., 2001, Vol. 153, pp. 75-86 [Abstract] [Article] [Predicted Structure]

    2000

  47. Jun Xing, Willy Wriggers, Geraldine M. Jefferson, Richard Stein, Herbert C. Cheung, and Steven S. Rosenfeld. Kinesin Has Three Nucleotide-Dependent Conformations - Implications for Strain-Dependent Release. J. Biol. Chem., 2000, Vol. 275, pp. 35413-35423 [Abstract] [Article]

  48. Willy Wriggers, Rajendra K. Agrawal, Devin Lee Drew, J. Andrew McCammon, and Joachim Frank. Domain Movements of EF-G bound to the 70S Ribosome: Insights from a Hand-Shaking between Multi-Resolution Structures. Biophysical Journal, 2000, Vol. 79, pp. 1670-1678. [Abstract] [Article] [Updated Link]

  49. Eldar Kim, Willy Wriggers, Martin Phillips, Kevin Kokabi, Peter Rubenstein, and Emil Reisler. Cross-Linking Constraints on F-actin Structure. J. Molec. Biol., 2000, Vol. 299, pp. 421-429. [Abstract] [Article] [Predicted Structures]

    1999

  50. Xiaoyi Yao, Stephanie Grade, Willy Wriggers, and Peter Rubenstein. His73, Often Methylated, Is an Important Structural Determinant for Actin - A Mutagenic Analysis of H73 of Yeast Actin. J. Biol. Chem., 1999, Vol. 274, pp. 37443-37449. [Abstract] [Article] [Predicted Structures]

  51. Willy Wriggers, Ronald A. Milligan, and J. Andrew McCammon. Situs: A Package for Docking Crystal Structures into Low-Resolution Maps from Electron Microscopy. J. Structural Biology, 1999, Vol. 125, pp. 185-195. [Abstract] [Article] [JSB Paper of the Year Award] [Updated Link]

  52. Willy Wriggers and Klaus Schulten. Investigating a Back Door Mechanism of Actin Phosphate Release by Steered Molecular Dynamics. Proteins: Structure, Function, and Genetics, 1999, Vol. 35, pp. 262-273. [Abstract] [Article]

  53. Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers, and Klaus Schulten. Steered Molecular Dynamics. Chapter in "Computational Molecular Dynamics: Challenges, Methods, Ideas", Springer Verlag, 1999 [Abstract] [Article]

    1998

  54. Willy Wriggers, Ronald A. Milligan, Klaus Schulten, and J. Andrew McCammon. Self-Organizing Neural Networks Bridge the Biomolecular Resolution Gap. J. Molecular Biology, 1998, Vol. 284, pp. 1247-1254. [Abstract] [Article]

  55. Willy Wriggers, Jay X. Tang, Toshifumi Azuma, Peter Marks, and Paul A. Janmey. Cofilin and Gelsolin Segment-1: Molecular Dynamics Simulation and Biochemical Analysis Predict a Similar Actin Binding Mode. J. Molecular Biology, 1998, Vol. 282, pp. 921-932. [Abstract] [Article] [Predicted Structure]

  56. Willy Wriggers and Klaus Schulten. Nucleotide-Dependent Movements of the Kinesin Motor Domain Predicted by Simulated Annealing. Biophysical Journal, 1998, Vol. 75, pp. 646-661. [Abstract] [Article] [Predicted Structures]

  57. Willy Wriggers, Ernest Mehler, Felicia Pitici, Harel Weinstein, and Klaus Schulten. Structure and Dynamics of Calmodulin in Solution. Biophysical Journal 1998, Vol. 74, pp. 1622-1639. [Abstract] [Article]


    58. 1997

  58. James C. Phillips, Willy Wriggers, Zhigang Li, Ana Jonas and Klaus Schulten. Predicting the Structure of Apolipoprotein A-I in Reconstituted High Density Lipoprotein Disks. Biophysical Journal 1997, Vol. 73, pp. 2337-2346. [Abstract] [Article]

  59. Willy Wriggers and Klaus Schulten. Protein Domain Movements: Detection of Rigid Domains and Visualization of Effective Rotations in Comparisons of Atomic Coordinates. Proteins: Structure, Function, and Genetics 1997, Vol. 29, pp. 1-14. [Abstract] [Article] [Updated Link]

  60. Willy Wriggers and Klaus Schulten. Stability and Dynamics of G-actin: Back Door Water Diffusion and Behavior of a Subdomain 3/4 Loop. Biophysical Journal 1997, Vol. 73, pp. 624-639. [Abstract] [Article] [Nucleotide Parameters]

    61. 1996

  61. Manel A. Balsera, Willy Wriggers, Yoshitsugu Oono, and Klaus Schulten. Principal Component Analysis and Long Time Protein Dynamics. Journal of Physical Chemistry 1996, Vol. 100, pp. 2567-2572. [Abstract] [Article]

    1991


  62. Willy Wriggers. Deterministisches Chaos und Himmelsmechanik: Teil 1 (Deterministic Chaos and Celestial Mechanics: Part 1). Rosa Ursina (Quarterly Magazine of the Astronomischer Arbeitskreis Ingolstadt, Germany) 1991, Issue 03 (July), pp. 8-16. [Article] [Personal Commentary]

  63. Willy Wriggers. Deterministisches Chaos und Himmelsmechanik: Teil 2 (Deterministic Chaos and Celestial Mechanics: Part 2). Rosa Ursina (Quarterly Magazine of the Astronomischer Arbeitskreis Ingolstadt, Germany) 1991, Issue 04 (October), pp. 8-17. [Article] [Personal Commentary]

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