Probik: Protein backbone motion by inverse kinematics

International Journal of Robotics Research

Volumn 24, Issue 11, 2005, Pages 971-982

  Noonan, Kimberly ^a   O'Brien, David ^a   Snoeyink, Jack ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Backbone geometry; Denavit Hartenberg frames; Protein design; Six revolute joint manipulator

Indexed keywords

BIOCHEMISTRY; BIOTECHNOLOGY; DERIVATIVES; INVERSE KINEMATICS; MANIPULATORS;

BACKBONE GEOMETRY; DENAVIT-HARTENBERG FRAMES; PROTEIN DESIGN; SIX REVOLUTE JOINT MANIPULATOR;

PROTEINS;

EID: 27744550789     PISSN: 02783649     EISSN: None     Source Type: Journal    
DOI: 10.1177/0278364905059108     Document Type: Conference Paper

References (35)

1. Amadei, A. et al. 1996. An efficient method for sampling the essential subspace of proteins. Journal of Biomolecular Structure Dynamics 13(4):615-625.
2. Branden C. and Tooze J. 1999. Introduction to Protein Structure, 2nd edition, Garland Publishing, New York.
3. Braun, W. 1987. Local deformation studies of chain molecules: Differential conditions for changes of dihedral angles. Biopolymers 26(10):1691-1704
4. Bruccoleri, R. E. and Karplus, M. 1985. Chain closure with bond angle variations. Macromolecules 18:2767-2773.
5. Canutescu, A. A. and Dunbrack, R. L. Jr. 2003. Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein Science 12:963-972.
6. Coutsais, E. A., Seok, C., Jacobson, M. P., and Dill, K. A. 2004. A kinematic view of loop closure. Journal of Computational Chemistry 25:510-528.
7. Davis, I. W., Murray, L. W., Richardson, J. S., and Richardson, D. C. 2004. MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Research 32(Web Server Issue):W615-619.
8. Davis, I. W., Arendall, W. B. III, Richardson, J. S., and Richardson, D. C. 2005. The Backrub: A gentle but rotamer-coupled mode of local backbone movement in proteins. In preparation.
9. de Groot, B. L. et al. 1996. Toward an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. Journal of Biomolecular Structure Dynamics 13(5):741-751.
10. Dwyer, M., Looger, L., and Hellinga, H. 2004. Computational design of a biologically active enzyme. Science 304:1967-1971.
11. Edelsbrunner H. and Koehl P. 2003. The weighted volume derivative of a space-filling diagram. Proceedings of the National Academy of Science 100:2203-2208.
12. Engh R. A. and Huber, R. 1991. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallographica A47:392-400.
13. Go, N. and Scheraga, H. A. 1970. Ring closure and local conformational deformations of chain molecules. Macromolecules 3:178-186.
14. Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J. F., Honig, B., Shaw, D. E., and Friesner, R. A. 2004. A hierarchical approach to all-atom protein loop prediction. Proteins: Structure, Function, and Bioinformatics 55(2):351-367
15. Jolliffe, I. T. 2002. Principal Component Analysis, Springer-Verlag, New York.
16. Kobayashi, N., Yamato, T., and Go, N. 1997. Mechanical property of a TIM-barrel protein. Proteins 28(1):109-116.
17. Kolodny, R., Guibas, L., Levitt, M., and Koehl, P. 2005. Inverse kinematics in biology: The protein loop closure problem. International Journal of Robotics Research 24(2-3):151-163.
18. Leach, A. R. 1996. Molecular Modelling: Principles and Applications, Addison-Wesley Longman, Reading, MA.
19. Looger, L., Dwyer, M., Smith, J., and Hellinga, H. 2003. Computational design of receptor and sensor proteins with novel functions. Nature 423(6936):185-190.
20. Lotan, I., van den Bedem, H., Deacon, A. M., and Latombe, J.-C. 2005. Computing protein structures from electron density maps: The missing fragment problem. Algorithmic Foundations of Robotics VI, STAR 17, M. Erdmann, D. Hsu, M. Overmars, F. van der Stappen, editors, Springer-Verlag, Berlin.
21. Lovell, S. et al. 2003. Structure validation by Cα Geometry: φ, ψ and Cβ deviation. Proteins: Structure, Function, and Genetics 50:437-450. See http://kinemage.biochem.duke.edu/validation/model.html.
22. Manocha, D. and Canny, J. 1992. Real-time inverse kinematics for general 6R manipulators. Proceedings of the IEEE International Conference on Robotics and Automation, Nice, France, pp. 383-389.
23. Manocha, D. and Canny, J. 1994. Efficient inverse kinematics of general 6R manipulators. IEEE Transactions on Robotics and Automation 10(5):648-657.
24. Manocha, D. and Zhu, Y. 1994. A fast algorithm and system for inverse kinematics of general serial manipulators. Proceedings of the IEEE Conference on Robotics and Automation, San Diego, CA, pp. 3348-3354.
25. Palmer, K. A. and Scheraga, H. A. 1991. Standard-geometry chains fitted to X-ray derived structures: Validation of the rigid-geometry approximation. I. Chain closure through a limited search of "loop" conformations. Journal of Computational Chemistry 12(4):505-526.
26. Petsko, G. A. and Ringe, D. 2004. Protein Structure and Function, New Science Press, Oxford.
27. Raghavan, M. and Roth, B. 1989. Kinematic analysis of the 6R manipulator of general geometry. International Symposium on Robotics Research, Tokyo, Japan, pp. 314-320.
28. Richardson, D. C. and Richardson, J. S. 2001. MAGE, PROBE, and Kinemages. International Tables for Crystallography, M. G. Rossmann and E. Arnold, editors, Kluwer, Dordrecht, Vol. F, Chapter 25.2.8., pp. 727-730.
29. Sommese, A. J. and Wampler, C. W. II. 2005. The Numerical Solution of Systems of Polynomials Arising in Engineering and Science, World Scientific, Singapore.
30. Song, G. and Amato, N. M. 2001. A motion planning approach to folding: From paper craft to protein folding. Proceedings of the IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea, May 21-26, pp. 948-953.
31. Teodoro M. L., Phillips, G. N. Jr., and Kavraki, L. E. 2001. Molecular docking: A problem with thousands of degrees of freedom. Proceedings of the IEEE International Conference on Robotics and Automation (ICRA), Seoul, Korea, May 21-26, pp. 960-965.
32. Teodoro M. L., Phillips, G. N. Jr., and Kavraki, L. E. 2003. Understanding protein flexibility through dimensionality reduction. Journal of Computational Biology 10(3-4):617-634.
33. Wampler, C. W. II and Morgan, A. P. 1993. Solving the kinematics of general 6R manipulators using polynomial continuation. Robotics: Applied Mathematics and Computational Aspects, K. Warwick, editor, Clarendon, Oxford, pp. 57-69.
34. Wedemeyer, W. and Scheraga, H. 1999. Exact analytical loop closure in proteins using polynomial equations. Journal of Computational Chemistry 20:819-844.
35. Zhang, M. and Kavraki, L. E. 2002. Solving molecular inverse kinematics problems for protein folding and drug design Currents in Computational Molecular Biology, RECOMB '02, Washington, DC, USA, pp. 214-215.