Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turns

Proteins: Structure, Function and Genetics

Volumn 29, Issue 4, 1997, Pages 443-460

  Hu, Wei Ping ^a   Kolinski, Andrzej ^a,b   Skolnick, Jeffrey ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WARSAW   (Poland)

Author keywords

Fourier transform; Local interactions; Protein folding; Secondary structure prediction; Statistical potential; Turn prediction

Indexed keywords

ACCURACY; ARTICLE; DIAGNOSTIC APPROACH ROUTE; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; DATA INTERPRETATION, STATISTICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0030719433     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199712)29:4<443::AID-PROT5>3.0.CO;2-9     Document Type: Article

References (26)

1. Richardson, J. The anatomy and taxonomy of protein structure. Adv. Prot. Chem. 34:167-339, 1981.
2. Kolinski, A., Skolnick, J., Godzik, A., Hu, W.P. A method for the prediction of surface "U"-turns and transglobular connections in small proteins. Proteins 27:290-308, 1997.
3. Skolnick, J., Kolinski, A., Ortiz, A.R. MONSSTER: A method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265:217-241, 1997.
4. Ortiz, A.R., Hu, W.P., Kolinski, A., Skolnick, J. A method for prediction of the low resolution tertiary structure of small proteins. J. Mol. Graph., in press, 1997.
5. Kolinski, A., Milik, M., Skolnick, J. A reduced model of short range interactions in polypeptide chains. J. Chem. Phys. 103:4312-4323, 1995.
6. Cohen, F.E., Abarbanel, R.M., Kuntz, I.D., Fletterick, R.J. Turn prediction in proteins using a pattern-matching approach. Biochemistry 25:266-275, 1986.
7. Gonzalez, R.C., Wintz, P. "Digital Image Processing." 2nd. edit. Menlo Park, CA: Addison Wesley, 1987:61-109.
8. Skolnick, J., Jaroszewski, L., Kolinski, A., Godzik, A. Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci. 6:676-688, 1997.
9. Kabsch, W., Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
10. Kolinski, A., Skolnick, J. Monte Carlo simulation of protein folding. I. Lattice model and interaction scheme. Proteins 18:338-352, 1994.
11. Sander, C., Schneider, R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-58, 1991.
12. Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-72, 1994.
13. Rost, B., Sander, C. Progress of 1D protein structure prediction at last. Proteins 23:295-300, 1996.
14. Bernstein, F.C., Koetzle, T.F., William, G.J.B., et al. The Protein Data Bank: A computer-based archival file for macromolecule structures. J. Mol. Biol. 112:535-542, 1977.
15. The prediction program and related information can be found in our group World-Wide Web server at "http://moray3.scripps.edu/newll/."
16. Matthews, B.W. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta 405:442-451, 1975.
17. Rose, G.D. Prediction of chain turns in globular proteins on a hydrophobic basis. Nature 272:589-590, 1978.
18. Rose, G.D., Gierasch, L.M., Smith, J.A. Turns in peptides and proteins. Adv. Protein Chem. 37:1-109, 1985.
19. Wilmot, C.M., Thornton, J.M. Analysis and prediction of the different types of β-turns in proteins. J. Mol. Biol. 203:221-232, 1988.
20. Rooman, M.J., Wodak, S.J., Thornton, J.M. Amino acid sequence templates derived from recurrent turn motifs in proteins: critical evaluation of their predictive power. Protein Eng. 3:23-27, 1989.
21. Hutchinson, E.G., Thornton, J.M. A revised set of potentials for β-turn formation in proteins. Protein Sci. 3:2207-2216, 1994.
22. Ohage, E.C., Graml, W., Walter, N.M., Steinbacher, S., Steipe, B. β-turn propensities as paradigms for the analysis of structural motif to engineer protein stability. Protein Sci. 6:233-241, 1997.
23. Chou, P.Y., Fasman, G.D. Empirical predictions of protein conformation. Annu. Rev. Biochem. 47:251-276, 1978.
24. Unger, R., Moult, J. Local interactions dominate folding in a simple protein model. J. Mol. Biol. 259:988-994, 1996.
25. Aurora, R., Creamer, T.P., Srinivasan, R., Rose, G.D. Local interactions in protein folding: Lessons from the alpha-helix. J. Biol. Chem. 272:1413-1416, 1997.
26. Srinivasan, R., Rose, G.D. LINUS: A hierarchic procedure to predict the fold of a protein. Proteins 22:81-99, 1995.