Biomachina Publications and Supplementary Data

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Journal Articles:

Submitted

  1. Sharon Grayer Wolf, Dalia Rivenzon-Segal, Willy Wriggers and Amnon Horovitz. Three-dimensional cryo-EM model of the D155A GroEL mutant reveals structural changes associated with its sequential intra-ring allosteric transitions. J. Mol. Biol. Submitted.

  2. Zhiyong Zhang and Willy Wriggers. Sparsification of Local Multivariate Features from Molecular Dynamics Trajectories. Proteins: Structure, Function, and Bioinformatics. Submitted.

  3. Jochen Heyd and Willy Wriggers. Hessian Filtering for Docking of Atomic Structures into 3D Cryo-Electron Microscopy Reconstructions. Biophysical Journal. Submitted.

In Press

Published

  1. 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]

  2. 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]

    3. 2006

  3. 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]

  4. 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]

  5. 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]

    6. 2005

  6. 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]

  7. 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]

  8. 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]

  9. 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]

    10. 2004

  10. 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]

  11. 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]

  12. 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]

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

    14. 2003

  14. 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]

  15. 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]

  16. 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]

  17. 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]

  18. 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]

  19. 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]

    20. 2002

  20. 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]

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

  22. 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] 

  23. 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]

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

    2001

  25. 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] [New Link]

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

  27. 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] [New Links: 1 2]

  28. 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

  29. 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]

  30. 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] [New Link]

  31. 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

  32. 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]

  33. 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] [New Link]

  34. 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]

  35. 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

  36. 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]

  37. 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]

  38. 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] 

  39. 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]

    40. 1997

  40. 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]

  41. 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] [New Link]

  42. 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 - 27MB] [Nucleotide Parameters] 

    1996

  43. 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]

Ph.D. Thesis:

Willy Wriggers. Structure, Function, and Dynamics of Cell Motility Proteins. University of Illinois at Urbana-Champaign, 1998. [PDF file, 183 pages]