Pose analysis of alpha-carbons in proteins

International Journal of Robotics Research

Volumn 24, Issue 2-3, 2005, Pages 183-210

  Lee, Sangyoon ^a   Chirikjian, Gregory S ^b  

^a Konkuk University   (South Korea)

^b Johns Hopkins University   (United States)

Author keywords

6D relative pose; Axis angle representation; Computational tool; Continuous distribution; Data visualization; Gaussian function; Interaction between residues; Protein data

Indexed keywords

AMINO ACIDS; CARBON; CONFORMATIONS; FUNCTIONS; HYDROPHOBICITY; MOLECULAR ORIENTATION; POLYPEPTIDES; PROBABILITY;

6D RELATIVE POSE; AXIS-ANGLE REPRESENTATION; COMPUTATIONAL TOOLS; CONTINUOUS DISTRIBUTION; DATA VISUALIZATION; GAUSSIAN FUNCTIONS; INTERACTION BETWEEN RESIDUES; PROTEIN DATA;

PROTEINS;

EID: 13444302536     PISSN: 02783649     EISSN: None     Source Type: Journal    
DOI: 10.1177/0278364905050353     Document Type: Article

References (20)

1. Bahar, I., and Jernigan, R. L. 1996. Coordination geometry of non-bonded residues in globular proteins. Folding and Design 1:357-370.
2. Banavar, J. R., Maritan, A., and Seno, F. 2002. Anisotropic effective interactions in a coarse-grained tube picture of proteins. Proteins 49:246-254.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. 2000. The protein data bank. Nucleic Acids Research 28:235-242.
4. Branden, C., and Tooze, J. 1999. Introduction to Protein Structure, 2nd edition, Garland Publishing, New York.
5. Buchete, N.-V., Straub, J. E., and Thirumalai, D. 2004a. Orienatation-dependent coarse-grained potentials by statistical analysis of molecular structural databases. Polymer 45:597-608.
6. Buchete, N.-V., Straub, J. E., and Thirumalai, D. 2004b. Orienatational potentials extracted from protein structures improve native fold recognition. Protein Science 13:862-874.
7. Buchete, N.-V., Straub, J. E., and Thirumalai, D. 2004c. Development of novel statistical potentials for protein fold recognition. Current Opinion in Structural Biology 14:1-8.
8. Chakrabarti, P., and Debnath, P. 2001. The interrelationships of side-chain and main-chain conformations in proteins. Progress in Biophysics and Molecular Biology 76:1-102.
9. Chirikjian, G. S., and Chétalet, O. 2002. Sampling and convolution on motion groups using generalized Gaussian functions. Electronic Journal of Computational Kinematics 1(1).
10. Chirikjian, G. S., and Kyatkin, A. B. 2000. Engineering Applications of Noncommutative Harmonic Analysis, CRC Press, Boca Raton, FL.
11. Kemp, J. P., and Chen, Z. Y. 1998. Formation of helical states in wormlike polymer chains. Physics Review Letter 81:3880-3883.
12. Kreyszig, E. 1999. Advanced Engineering Mathematics, 8th edition, Wiley, New York.
13. Kumar, S., and Nussinov, R. 1999. Salt bridge stability in monomeric proteins. Journal of Molecular Biology 293:1241-1255.
14. Lee, S., Fichtinger, G., and Chirikjian, G. S. 2002. Numerical algorithms for spatial registration of line fiducials from cross-sectional images. Medical Physics 29(8):1881-1891.
15. Lee, S. 2002. Pose Analysis in Image Registration and Protein Statistics. PhD Dissertation, Johns Hopkins University.
16. Lesk, A. M. 2001. Introduction to Protein Architecture, Oxford University Press, New York.
17. Murray, R. M., Li, Z., and Sastry, S. S. 1994. A Mathematical Introduction to Robotic Manipulation, CRC Press, Boca Raton, FL.
18. Ramachandran, G. N., and Sasisekharan, V. 1968. Conformation of polypeptides and proteins. Advances in Protein Chemistry 23:283-437.
19. Trovato, A., Ferkinghoff-Borg, J., and Jensen, M. H. 2003. Compact phases of polymers with hydrogen bonding. Physics Review E 67:021805.
20. Varshalovich, D. A., Moskalev, A. N., and Khersonskii, V. K. 1988. Quantum Theory of Angular Momentum, World Scientific, Singapore.