| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
Reprint requests to: Roland L. Dunbrack Jr., Institute for Cancer Research, Fox Chase Cancer Center, 7701 Burholme Avenue, Philadelphia, PA 19111, USA; e-mail: RL_Dunbrack{at}fccc.edu; fax: (215) 728-2412.
In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable and fail to converge. We present an algorithm developed originally for inverse kinematics applications in robotics. In robotics, an end effector in the form of a robot hand must reach for an object in space by altering adjustable joint angles and arm lengths. In loop prediction, dihedral angles must be adjusted to move the C-terminal residue of a segment to superimpose on a fixed anchor residue in the protein structure. The algorithm, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C-terminal anchor and the corresponding atoms in the fixed C-terminal anchor. The result is an equation in one variable for the proposed change in each dihedral. The algorithm proceeds iteratively through all of the adjustable dihedral angles from the N-terminal to the C-terminal end of the loop. CCD is suitable as a component of loop prediction methods that generate large numbers of trial structures. It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average.
Keywords: Homology modeling; loop modeling; protein structure prediction; inverse kinematics; robotics; cyclic coordinate descent; loop closure
CiteULike 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  S. Montgomerie, J. A. Cruz, S. Shrivastava, D. Arndt, M. Berjanskii, and D. S. Wishart PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation Nucleic Acids Res., July 1, 2008; 36(suppl_2): W202 - W209. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. S. Wishart, D. Arndt, M. Berjanskii, P. Tang, J. Zhou, and G. Lin CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data Nucleic Acids Res., July 1, 2008; 36(suppl_2): W496 - W502. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. S. Gangabadage, J. Zdunek, M. Tessari, S. Nilsson, G. Olivecrona, and S. S. Wijmenga Structure and Dynamics of Human Apolipoprotein CIII J. Biol. Chem., June 20, 2008; 283(25): 17416 - 17427. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Shehu, L. E. Kavraki, and C. Clementi Unfolding the fold of cyclic cysteine-rich peptides Protein Sci., March 1, 2008; 17(3): 482 - 493. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 X. Hu, H. Wang, H. Ke, and B. Kuhlman High-resolution design of a protein loop PNAS, November 6, 2007; 104(45): 17668 - 17673. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Luque, I. Saugar, J. F. Rodriguez, N. Verdaguer, D. Garriga, C. S. Martin, J. A. Velazquez-Muriel, B. L. Trus, J. L. Carrascosa, and J. R. Caston Infectious Bursal Disease Virus Capsid Assembly and Maturation by Structural Rearrangements of a Transient Molecular Switch J. Virol., July 1, 2007; 81(13): 6869 - 6878. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Shehu, L. E. Kavraki, and C. Clementi On the Characterization of Protein Native State Ensembles Biophys. J., March 1, 2007; 92(5): 1503 - 1511. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Zhao, D. Stoffler, and M. Sanner Hierarchical and multi-resolution representation of protein flexibility Bioinformatics, November 15, 2006; 22(22): 2768 - 2774. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Chivian and D. Baker Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection Nucleic Acids Res., October 18, 2006; 34(17): e112 - e112. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. N. Offman, P. W. Fitzjohn, and P. A. Bates Developing a move-set for protein model refinement Bioinformatics, August 1, 2006; 22(15): 1838 - 1845. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Noonan, D. O'Brien, and J. Snoeyink Probik: Protein Backbone Motion by Inverse Kinematics The International Journal of Robotics Research, November 1, 2005; 24(11): 971 - 982. [Abstract] [PDF]
|
|
|
|
|
|
Y. Inbar, H. J. Wolfson, and R. Nussinov Multiple Docking for Protein Structure Prediction The International Journal of Robotics Research, February 1, 2005; 24(2-3): 131 - 150. [Abstract] [PDF]
|
|
|
|
|
|
R. Kolodny, L. Guibas, M. Levitt, and P. Koehl Inverse Kinematics in Biology: The Protein Loop Closure Problem The International Journal of Robotics Research, February 1, 2005; 24(2-3): 151 - 163. [Abstract] [PDF]
|
|
|
|
|
|
G. Wang and R. L. Dunbrack Jr. Scoring profile-to-profile sequence alignments Protein Sci., June 1, 2004; 13(6): 1612 - 1626. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
