Energy minimization studies on α-turns

Journal of Peptide Science

Volumn 4, Issue 4, 1998, Pages 239-252

  Ramakrishnan, C ^a   Nataraj, D V ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

Energy minimization; Hydrogen bonded tetrapeptide; Secondary structure; turn conformation; turns

Indexed keywords

GLYCINE; OLIGOPEPTIDE; PROLINE;

ARTICLE; AUTOMATED PATTERN RECOGNITION; CHEMICAL STRUCTURE; CHEMISTRY; ENERGY METABOLISM; HYDROGEN BOND; PROTEIN SECONDARY STRUCTURE;

ENERGY METABOLISM; GLYCINE; HYDROGEN BONDING; MODELS, MOLECULAR; OLIGOPEPTIDES; PATTERN RECOGNITION, AUTOMATED; PROLINE; PROTEIN STRUCTURE, SECONDARY;

EID: 0032084287     PISSN: 10752617     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1099-1387(199806)4:4<239::AID-PSC140>3.0.CO;2-F     Document Type: Article

References (19)

1. D. V. Nataraj, N. Srinivasan, R. Sawdhamini and C. Ramakrishnan (1995). Curr. Sci. (India) 69, 434-447.
2. C. M. Venkatachalam (1968). Stereochemlcal criteria for polypeptides and proteins. Conformation of a system of three linked peptide units. Biopolymers 6, 1425-1436.
3. R. Chandrasekaran, A. V. Lakshminarayanan, U. V. Pandya and G. N. Ramachandran (1974). Conformation of the LL and LD hairpin bends with internal hydrogen bonds in peptides and proteins. Biochim. Biophys. Acta 303, 14-27.
4. R. B. Corey and L. Pauling (1953). Dimensions of polypeptide chains. Proc. R. Soc. (London) B141, 10-20.
5. G. N. Ramachandran and V. Sasisekharan (1968). Conformation of polypeptides and proteins. Acta. Protein Chem. 23, 283-437.
6. P. K. C. Paul and C. Ramakrishnan (1985). Studies on hydrogen bonds Part V - Hydrogen bonding in energy minimization studies of peptide. J. Biomol. Structure Dynamics 2, 879-989.
7. W. Murray in: Numerical Methods for Unconstrained Optimization, Academic Press, London 1972.
8. S. R. Niketic and K. Rasmussen in: Lecture Notes in Chemistry. Vol. 3, Springer Verlag 1977.
9. R. Fletcher in: Practical Methods of Optimization, Wiley, New York 1980.
10. P. Y. Chou and G. D. Fasman (1977). β-Turns in Proteins. J. Mol. Biol. 115, 135-175.
11. J. S. Richardson (1981). The anatomy and taxonomy of protein structure. Adv. Protein Chem. 34, 167-339.
12. G. D. Rose, L. M. Gierasch and J. A. Smith (1985). Turns in peptides and proteins. Adv. Protein Chem. 37, 1-109.
13. C. M. Wilmot and J. M. Thornton (1988). Analysis and prediction of the different types of β-turn in proteins. J. Mol. Biol. 203, 221-232.
14. V. N. Balaji, PhD Thesis Molecular Biophysics Unit, Indian Institute of Science, Bangalore 1980.
15. M. J. O. Anteunis and J. J. M. Sleekx in: Molecular Structure and Energetics, p. 189, Vol. 4, J. F. Leibman and A. Greenberg Eds., VCH Publishers Inc. (1987).
16. J. S. Richardson and D. C. Richardson (1989). The de novo design of protein structures. Trends Biochem. Sci. 14, 304-309.
17. D. V. Nataraj, PhD Thesis Molecular Biophysics Unit, Indian Institute of Science, Bangalore 1996.
18. F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice Jr, J. R. Rodgers, O. Kennard, T. Shimanouchi and M. Tasumi (1977). The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
19. K. Gunasekaran, C. Ramakrishnan and P. Balaram (1997). β-Hairpins in proteins revisited: Lessons for de novo design. Prof. Eng. (in press).