The simbios national center: Systems biology in motion

Proceedings of the IEEE

Volumn 96, Issue 8, 2008, Pages 1266-1280

  Schmidt, Jeanette P ^b   Delp, Scott L ^c   Sherman, Michael A ^b   Taylor, Charles A ^a,b   Pande, Vijay S ^c   Altman, Russ B ^c  

^a IEEE

^b Stanford University   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

Biomedical computation; Cardiovascular dynamics; Dynamics; Neuromuscular biomechanics; Physics based; Protein folding; RNA folding; Simulation

Indexed keywords

BIOLOGICAL SYSTEMS; BIOMECHANICS; DYNAMICS; FLOW OF FLUIDS; INFORMATION DISSEMINATION; PROTEIN FOLDING;

BIOMEDICAL COMPUTATIONS; CARDIOVASCULAR DYNAMICS; PHYSICS-BASED; RNA FOLDING; SIMULATION;

BIOINFORMATICS;

EID: 47949114719     PISSN: 00189219     EISSN: None     Source Type: Journal    
DOI: 10.1109/JPROC.2008.925454     Document Type: Article

References (44)

1. F. E. Zajac, "Muscle coordination of movement: A perspective, " J. Biomechanics, vol. 26, pp. 109-124, 1993.
2. R. Russell and D. Herschlag, "Probing the folding landscape of the tetrahymena ribozyme: Commitment to form the native conformation is late in the folding pathway," J. Mol. Biol., vol. 308, no. 5, pp. 839-851, 2001.
3. A. Laederach, L. I. Shcherbakova, M. Liang, M. Brenowitz, and R. B. Altman, "Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule," J. Mol. Biol., vol. 358, no. 4, pp. 1179-1190, May 2006.
4. A. Houdusse, A. G. Szent-Gyorgyi, and C. Cohen, "Three conformational states ACofscallop myosin S1," Proc. Natl. Acad. Sci. USA 97, pp. 11 238-11 243, 2000.
5. B. K. Shoichet, S. L. McGovern, B. Wei, and J. J. Irwin, "Lead discovery using molecular docking," Current Opinion in Chemical Biology, vol. 6, pp. 439-446, 2002.
6. D. E. Clark, "Rapid caclulation of polar molecular surface area and its application to the prediction of transport phenomena," J. Pharmaceutical Sciences, vol. 88, pp. 807-814, 2000.
7. T. Hansson, C. Oostenbrink, and W. F. van Gunsteren, "Molecular dynamics simulations," Current Opinion in Structural Biology, vol. 12, pp. 190-196, 2002.
8. C. D. Snow, H. Nguyen, V. S. Pande, and M. Gruebele, "Absolute comparison of simulated and experimental protein-folding dynamics," Nature, vol. 420, pp. 102-106, 2002.
9. M. Karplus and A. McCammon, "Molecular dynamics simulations of biomolecules," Nature Structural Biology, vol. 9, pp. 646-652, 2002.
10. M. Tomita, "Whole-cell simulation: A grand challenge of the 21st century," Trends in Biotechnology, vol. 19, no. 6, pp. 205-210, 2001.
11. R. Y. Kwon, A. J. Lew, and C. R. Jacobs, "A microstructurally informed model for the mechanical response of three-dimensional actin networks," Computer Methods in Biomechanics and Biomedical Engineering, to appear.
12. D. G. Thelen, F. C. Anderson, and S. L. Delp, "Generating forward dynamic simulations of movement using computed muscle control," J. Biomech., vol. 36, pp. 321-328, 2003.
13. C. A. Taylor and M. T. Draney, "Experimental and computational methods in cardiovascular fluid mechanics," Annual Review of Fluid Mechanics, vol. 36, pp. 197-231, 2004.
14. S. Delp and J. P. Loan, "A graphics-based software system to develop and analyze models of musculoskeletal structures, " Computer in Biology and Medicine, vol. 25, no. 1, pp. 21-34, 1995.
15. M. A. Puso, B. N. Maker, R. M. Ferencz, and J. O. Hallquist, "Nike3d: A Nonlinear, Implicit, Three-Dimensional Finite Element Code for Solid and Structural Mechanics, 2002, Lawrence Livermore National Lab Technical Report.
16. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, "CHARMM: A program for macromolecular energy minimization and dynamics," J. Comp. Chem., vol. 4, pp. 187-217, 1983.
17. C. Keasar and R. Rosenfeld, "Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations," Fold. Des., vol. 3, no. 5, pp. 379-88, 1998.
18. P. Ren and J. W. Ponder, "Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation," J. Phys. Chem. B, vol. 107, pp. 5933-5947, 2003.
19. R. V. Pappu, R. K. Hart, and J. W. Ponder, "Analysis and application of potential energy smoothing for global optimization," J. Phys. Chem. B, vol. 102, pp. 9725-9742, 1998.
20. Y. Kong and J. W. Ponder, "Reaction field methods for off-center multipoles," J. Chem. Phys., vol. 107, pp. 481-492, 1997.
21. H. J. C. Berendsen, D. van der Spoel, and R. van Drunen, "GROMACS: A message-passing parallel molecular dynamics implementation," Comp. Phys. Comm., vol. 91, pp. 43-56, 1995.
22. E. Lindahl, B. Hess, and D. van der Spoel, "GROMACS 3.0: A package for molecular simulation and trajectory analysis," J. Mol. Mod., vol. 7, pp. 306-317, 2001.
23. C. D. Schwieters and G. M. Clore, "Internal coordinates for molecular dynamics and minimization in structure determination and refinement," J. Mag. Res., vol. 152, no. 2, pp. 288-302, 2001.
24. K. S. Chang and O. Khatib, "Efficient algorithm for extended operational space inertia matrix," in Proc. 1999 IEEE/RS/ Intl. Conf., on Intelligent Robots and Systems, 1999.
25. A. Jain, N. Vaidehi, and G. A. Rodriguez, "Fast recursive algorithm for molecular dynamics simulation," J. Comput. Phys., vol. 106, no. 2, pp. 258-268, 1993.
26. N. Vaidehi, A. Jain, and W. A. Goddard, "Constant temperature constrained molecular dynamics: The newton-euler inverse mass operator method," J. Phys. Chem., vol. 100, no. 25, pp. 10 508-10 517, 1996.
27. P. A. Golubkov and P. Ren, "Generalized coarse-grained model based on point multipole and Gay-Berne potentials," J. Chem. Phys., vol. 125, p. 064103, 2006.
28. S. D. Cohen and A. C. Hindmarsh, "CVODE, a stiff/nonstiff ODE solver in C," Computers in Physics, vol. 10, no. 2, pp. 138-143, 1996.
29. S. L. Delp, J. P. Loan, M. G. Hoy, F. E. Zajac, E. L. Topp, and J. M. Rosen, "An interactive graphics-based model of the lower extremity to study orthopaedic surgical procedures," IEEE Trans. Biomedical Engineering, vol. 37, no. 8, pp. 757-767, 1990.
30. S. L. Delp, F. C. Anderson, A. S. Arnold, J. P Loan, A. Habib, C. John, E. Guendelman, and D. G. Thelen, "OpenSim: Open-source software to create and analyze dynamic simulations of movement," IEEE Trans. Biomedical Engineering, vol. 54, no. 11, pp. 1940-1950, 2007.
31. F. C. Anderson and M. G. Pandy, "Dynamic optimization of human walking," J. Biomech. Eng., vol. 123, no. 5, pp. 381-390, 2001.
32. T. R. Cech, "Self-splicing of group I introns," Annu. Rev. Biochem., vol. 59, pp. 543-568, 1990.
33. J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech, and J. A. Doudna, "Crystal structure of a group I ribozyme domain: Principles of RNA packing," Science, vol. 273, pp. 1678-1685, 1996.
34. B. L. Golden, A. R. Gooding, E. R. Podell, and T. R. Cech, "A preorganized active site in the crystal structure of the Tetrahymena ribozyme," Science, vol. 282, pp. 259-264, 1998.
35. D. Thirumalai and C. Hyeon, "RNA and protein folding: Common themes and variations," Biochemistry, vol. 44, pp. 4957-4970, 2005.
36. B. J. Tucker and R. R. Breaker, "Riboswitches as versatile gene control elements," Curr. Opin. Struct. Biol., vol. 15, pp. 342-348, 2005.
37. N. Ban, P. Nissen, J. Hansen, P. B. Moore, and T. A. Steitz, "The complete atomic structure of the large ribosomal subunit at 2.4 A resolution," Science, vol. 289, no. 5481, pp. 878-879, 2000.
38. B. T. Wimberly, D. E. Brodersen,
39. W. M. Clemons, Jr., R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T. Hartsch, and V. Ramakrishnan, "Structure of the 30S ribosomal subunit," Nature, vol. 407, pp. 327-339, 2000.
40. M. M. Yusupov, G. Z. Yusupova, A. Baucom, K. Lieberman, T. N. Earnest, J. H. Cate, and H. F. Noller, "Crystal structure of the ribosome at 5.5 A resolution," Science, vol. 292, pp. 883-896, 2001.
41. R. Das, A. Laederach, S. M. Pearlman, D. Herschlag, and R. B. Altman, "SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments," RNA, vol. 11, pp. 344-354, 2005.
42. C. J. Cramer and D. G. Truhlar, "Implicit solvation models: Equilibria, structure, spectra, dynamics," Chem. Rev., pp. 2161-2200, 1999.
43. E. Elsen, M. Houston, V. Vishal, E. Darve, P. Hanrahan, and V. S. Pande, "N-Body simulation on GPUs," in Proc. 2006 ACM/IEEE Conf. on Supercomputing, 2006, p. 188.
44. M. R. Shirts and V. S. Pande, "Screen savers of the world, unite!" Science, vol. 290, pp. 1903-1904, 2000.