The role of long-range interactions in defining the secondary structure of proteins is overestimated

Bioinformatics

Volumn 13, Issue 3, 1997, Pages 297-301

  Fiser, Andras ^a   Dosztanyi, Zsuzsanna ^a   Simon, Istvan ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RESIDUE ANALYSIS;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, FACTUAL; EVALUATION STUDIES; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE;

EID: 0030957127     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.3.297     Document Type: Article

References (24)

1. Barton, G.J. (1995) Protein secondary structure prediction. Current Opin. Struct. Bioi. 5, 372-376.
2. Bemstein.F.C, Koetzle.T.F. Williams.G.J.B.. Meyer.J.E.F., Brice.M.D.. RodgersJ.R.. Kennard.O., Shimanouchi.T and Tasumi.M. (1977) The protein data bank: a computer based archival file for macromolecular structure. J. Mol Biol. 112, 535-542.
3. Chou.P. and Fasman.G. (1978) Prediction of secondary structure of proteins from amino acid sequence. Adv. Enzvmol. Relal. Subj. Biochem., 47, 45-148.
4. Cohen.B.I., Presnell.S.R. and Cohen.F.E. (1993) Origins of structural diversity within sequentially identical hexapeptides. Protein Sci., 2, 2134-2145.
5. Deleage.G., Clerc.F.F., Roux.B. and Gautheron.D.C. (1988) Antheprot: a package for protein sequence analysis using a microcomputer. Comput. Applic. Biosci., 4, 351-356.
6. Fiser.A., Tusnady.G.E. and Simon, I. (1994) Chaos game representation of protein structures. J. Mol. Graph., 12, 302-304.
7. Fiser.A., Simon, I. and Barton.G.J. (1996) Conservation of amino acids in multiple alignments: aspartic acid has unexpected conservation. FEBS Lett., 397, 225-229.
8. Garnier.J., Osguthorpe.D.J. and Robson.B. (1978) Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J. Mol. Biol, 120, 97-120.
9. Heringa.J. and Argos.P. (1991) Side-chain clusters in protein structure and their role in protein folding. J. Mol. Biol., 220, 151-171.
10. Kabsch.A.W. and Sander.C. (1983) A dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
11. Kabsch.A.W. and Sander.C. (1984) On the use of sequence homologies to predict protein structure: identical pentapeptides can have completely different conformations. Proc. Natl. Acad. Sci. USA, 81, 1075-1078.
12. Miyazawa.S. and Jernigan.R.L. (1993) A new substitution matrix for protein sequence search based on contact frequencies in protein structures. Protein Eng., 6, 267-278.
13. Narayana.S.U.L. and Argos.P. (1984) Residue contacts in protein structures and implications for protein folding. Int. J. Peptide Protein Res., 24, 25-39.
14. Ptitsyn.O.B. and Finkelstein.A.V. (1983) Theory of protein secondary structure and algorithm of its prediction. Biopolymers, 22, 15-25.
15. Rackovsky.S. (1995) On the existence and implications of an inverse folding code in proteins. Proc. Natl. Acad. Sci. USA, 92, 6861-6863.
16. Rost.B. and Sander.C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
17. Russell, R.B. and Barton.G.J. (1994) Structural features can be unconserved in proteins with similar folds: An analysis of side-chain to side-chain contacts, secondary structure and accessibility J. Mol. Biol., 244, 332-350.
18. Schulz.G.E. and Schirmer.R.H. (1979) Principles of Protein Structure. Springer-Verlag, New York.
19. Shindyalov.I.N., Kolchanov.N.A. and Sander.C. (1994) Can three-dimensional contacts in protein structure be predicted by analysis of correlated mutations? Protein Eng., 7, 349-358.
20. Singh.J. and Thronton.J.M. (1992) Atlas of Protein Side-chain Interactions. Oxford University Press, New York.
21. Swindells.M.B. (1995) A procedure for the automatic determination of hydrophobic cores in protein structures. Protein Set., 4, 93-102.
22. Tudos.E., Fiser.A. and Simon, I. (1994) Different sequence environments of amino acid residues involved and not involved in long-range interactions. Int. J. Peptide Protein Res., 43, 205-208.
23. Wako.H., Saito.N. and Scheraga.H.A. (1983) Statistical mechanical treatment of alpha helices and extended structures in proteins with inclusion of short-and medium-range interactions. J. Protein Chem., 2, 221-249.
24. Wilson.I.A., Haft.D.H., Getzoff, E.D., Tainer.J.A., Lemer.R.A. and Brenner.S. (1985) Identical short peptide sequences in unrelated protein can have different conformations: a testing ground for theories of immune recognition. Proc. Natl. Acad. Sci. USA, 82. 5255-5259.