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Automated Illustration of Molecular Flexibility
January 2012 (vol. 18 no. 1)
pp. 132-145
ASCII Text
x 
 
Aaron Bryden, George N. Phillips Jr., Michael Gleicher, "Automated Illustration of Molecular Flexibility," IEEE Transactions on Visualization and Computer Graphics, vol. 18, no. 1, pp. 132-145, January, 2012.
 
 
BibTex
x
 
@article{ 10.1109/TVCG.2010.250,
author = {Aaron Bryden and George N. Phillips Jr. and Michael Gleicher},
title = {Automated Illustration of Molecular Flexibility},
journal ={IEEE Transactions on Visualization and Computer Graphics},
volume = {18},
number = {1},
issn = {1077-2626},
year = {2012},
pages = {132-145},
doi = {http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.250},
publisher = {IEEE Computer Society},
address = {Los Alamitos, CA, USA},
}
 
 
RefWorks Procite/RefMan/Endnote
x 
 
TY - JOUR
JO - IEEE Transactions on Visualization and Computer Graphics
TI - Automated Illustration of Molecular Flexibility
IS - 1
SN - 1077-2626
SP132
EP145
EPD - 132-145
A1 - Aaron Bryden,
A1 - George N. Phillips Jr.,
A1 - Michael Gleicher,
PY - 2012
KW - Illustration
KW - motion
KW - molecular visualization.
VL - 18
JA - IEEE Transactions on Visualization and Computer Graphics
ER -
 
Aaron Bryden, University of Wisconsin Madison, Madison
George N. Phillips Jr., University of Wisconsin Madison, Madison
Michael Gleicher, University of Wisconsin Madison, Madison
In this paper, we present an approach to creating illustrations of molecular flexibility using normal mode analysis (NMA). The output of NMA is a collection of points corresponding to the locations of atoms and associated motion vectors, where a vector for each point is known. Our approach abstracts the complex object and its motion by grouping the points, models the motion of each group as an affine velocity, and depicts the motion of each group by automatically choosing glyphs such as arrows. Affine exponentials allow the extrapolation of nonlinear effects such as near rotations and spirals from the linear velocities. Our approach automatically groups points by finding sets of neighboring points whose motions fit the motion model. The geometry and motion models for each group are used to determine glyphs that depict the motion, with various aspects of the motion mapped to each glyph. We evaluated the utility of our system in real work done by structural biologists both by utilizing it in our own structural biology work and quantitatively measuring its usefulness on a set of known protein conformation changes. Additionally, in order to allow ourselves and our collaborators to effectively use our techniques we integrated our system with commonly used tools for molecular visualization.

[1] M. Alexa, “Linear Combination of Transformations,” ACM Trans. Graphics, vol. 21, no. 3, pp. 380-387, 2002.
[2] S. Arya, D.M. Mount, N.S. Netanyahu, R. Silverman, and A.Y. Wu, “An Optimal Algorithm for Approximate Nearest Neighbor Searching Fixed Dimensions,” J. ACM, vol. 45, no. 6, pp. 891-923, 1998.
[3] J. Assa, Y. Caspi, and D. Cohen-Or, “Action Synopsis: Pose Selection and Illustration,” ACM Trans. Graphics, vol. 24, no. 3, pp. 667-676, 2005.
[4] I. Bahar and A. Rader, “Coarse-Grained Normal Mode Analysis in Structural Biology,” Current Opinion in Structural Biology, vol. 15, no. 5, pp. 586-592, Oct. 2005.
[5] M.B. Berry, E. Bae, T.R. Bilderback, M. Glaser, and G.N. PhillipsJr., “Crystal Structure of ADP/AMP Complex of Escherichia Coli Adenylate Kinase,” Proteins, vol. 62, no. 2, pp. 555-556, Feb. 2006.
[6] S. Bouvier-Zappa, V. Ostromoukhov, and P. Poulin, “Motion Cues for Illustration of Skeletal Motion Capture Data,” Proc. Fifth Int'l Symp. Non-Photorealistic Animation and Rendering, pp. 133-140, 2007.
[7] J. Collomosse, D. Rowntree, and P. Hall, “Rendering Cartoon-Style Motion Cues in Post-Production Video,” Graphical Models, vol. 67, no. 6, pp. 549-564, 2005.
[8] D.W.J. Cruickshank, “The Analysis of the Anisotropic Thermal Motion of Molecules in Crystals,” Acta Crystallographica, vol. 9, pp. 754-756, 1956.
[9] Q. Cui et al., Normal Mode Analysis: Theory and Applications to Biological and Chemical Systems. Taylor and Francis Group, 2006.
[10] J.E. Cutting, “Representing Motion in a Static Image: Constraints and Parallels in Art, Science, and Popular Culture,” Perception, vol. 31, no. 10, pp. 1165-1193, 2002.
[11] O.D. Lampe, I. Viola, N. Reuter, and H. Hauser, “Two-Level Approach to Efficient Visualization of Protein Dynamics,” IEEE Trans. Visualization and Computer Graphics, vol. 13, no. 6, pp. 1616-1623, Nov./Dec. 2007.
[12] R. Dony, J. Mateer, and J. Robinson, “Techniques for Automated Reverse Storyboarding,” Proc. IEE J. Vision, Image and Signal Processing, vol. 152, no. 4, pp. 425-436, Aug. 2005.
[13] E. Eyal, L. Yang, and I. Bahar, “Anisotropic Network Model: Systematic Evaluation and a New Web Interface,” Bioinformatics, vol. 22, no. 21, pp. 2619-2627, Nov. 2006.
[14] S. Flores, N. Echols, D. Milburn, B. Hespenheide, K. Keating, J. Lu, S. Wells, E.Z. Yu, M. Thorpe, and M. Gerstein, “The Database of Macromolecular Motions: New Features Added at the Decade Mark,” Nucleic Acids Research, vol. 34, pp. D296-D301, Oct. 2004.
[15] M. Gleicher and F. Liu, “Re-Cinematography: Improving the Camerawork of Casual Video,” ACM Trans. Multimedia Computing, Communications, and Applications, vol. 5, no. 1, pp. 1-28, 2008.
[16] D.B. Goldman, B. Curless, S.M. Seitz, and D. Salesin, “Schematic Storyboarding for Video Visualization and Editing,” ACM Trans. Graphics, vol. 25, no. 3, pp. 862-871, 2006.
[17] T. Götzelmann, K. Hartmann, and T. Strothotte, “Annotation of Animated 3D-Objects,” Proc. Simulation and Visualization, 2007.
[18] A. Hawkins and C.M. Grimm, “Camera Keyframing Using Linear Interpolation of Matrices,” J. Graphics, GPU, and Game Tools, vol. 12, no. 3, pp. 55-69, 2007.
[19] A. Joshi and P. Rheingans, “Illustration-Inspired Techniques for Visualizing Time-Varying Data,” Proc. IEEE Visualization, pp. 679-686, 2005.
[20] B. Kim and I. Essa, “Video-Based Nonphotorealistic and Expressive Illustration of Motion,” Proc. Computer Graphics Int'l Conf., pp. 32-35, 2005.
[21] C. Lee and A. Varshney, “Representing Thermal Vibrations and Uncertainty in Molecular Surfaces,” Proc. SPIE Conf. Visualization and Data Analysis, pp. 80-90, 2002.
[22] H. Löffelmann, L. Mroz, and E. Gröller, “Hierarchical Streamarrows for the Visualization of Dynamical Systems,” Proc. Eighth Eurographics Workshop Visualization in Scientific Computing, pp. 155-164, 1997.
[23] S. McCloud, Understanding Comics: The Invisible Art, Harper Penrennial/Kitchen Sink Books, 1993.
[24] J.G. McCoy, E. Bitto, C.A. Bingman, G.E. Wesenberg, R.M. Bannen, D.A. Kondrashov, and G.N. PhillipsJr., “Structure and Dynamics of Udp-Glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound Udp-Glucose and Utp,” J. Molecular Biology, vol. 366, no. 3, pp. 830-841, 2007.
[25] T. Mcloughlin, R.S. Laramee, R. Peikert, F.H. Post, and M. Chen, “Over Two Decades of Integration-Based Geometric Flow Visualization,” Computer Graphics Forum, vol. 29, no. 6, pp. 1807-1820., Sept. 2010.
[26] R.M. Murray, S.S. Sastry, and L. Zexiang, A Mathematical Introduction to Robotic Manipulation. CRC Press, Inc., 1994.
[27] J. Painter and E.A. Merritt, “Optimal Description of a Protein Structure in Terms of Multiple Groups Undergoing TLS Motion,” Acta Crystallographica, vol. 62, no. 4, pp. D439-D450, 2006.
[28] A. Pang, C. Wittenbrink, and S. Lodha, “Approaches to Uncertainty Visualization,” The Visual Computer, vol. 13, no. 8, pp. 370-390, 1997.
[29] J. Schmidt-Ehrenberg, D. Baum, and H. Hege, “Visualizing Dynamic Molecular Conformations,” Proc. IEEE Conf. Visualization, pp. 235-242, 2002.
[30] D.D. Seligmann and S. Feiner, “Automated Generation of Intent-Based 3D Illustrations,” Proc. ACM SIGGRAPH, vol. 25, pp. 123-132, 1991.
[31] P. Shirley and S. Marschner, Fundamentals of Computer Graphics. A.K. Peters, 2009.
[32] K. Suhre and Y.-H. Sanejouand, “Elnemo: A Normal Mode Web Server for Protein Movement Analysis and the Generation of Templates for Molecular Replacement,” Nucleic Acids Research, vol. 32, pp. W610-W614, July 2004.
[33] M. Tarini, P. Cignoni, and C. Montani, “Ambient Occlusion and Edge Cueing for Enhancing Real Time Molecular Visualization,” IEEE Trans. Visualization and Computer Graphics, vol. 12, no. 5, pp. 1237-1244, Sept./Oct. 2006.
[34] A. Telea and J. van Wijk, “Simplified Representation of Vector Fields,” Proc. 10th IEEE Visualization Conf., 1999.
[35] L.N. Trefethen and D. Bau III, Numerical Linear Algebra. SIAM: Soc. for Industrial and Applied Math., 1997.
[36] T. Van Walsum, F.H. Post, D. Silver, and F.J. Post, “Feature Extraction and Iconic Visualization,” IEEE Trans. Visualization and Computer Graphics, vol. 2, no. 2, pp. 111-119, June 1996.
[37] R. Xu and D. Wunsch II, “Survey of Clustering Algorithms,” IEEE Trans. Neural Networks, vol. 16, no. 3, pp. 645-678, May 2005.

Index Terms:
Illustration, motion, molecular visualization.
Citation:
Aaron Bryden, George N. Phillips Jr., Michael Gleicher, "Automated Illustration of Molecular Flexibility," IEEE Transactions on Visualization and Computer Graphics, vol. 18, no. 1, pp. 132-145, Jan. 2012, doi:10.1109/TVCG.2010.250
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