Prediction of protein secondary structure using the 3d-1d compatibility algorithm

Bioinformatics

Volumn 13, Issue 4, 1997, Pages 415-424

  Ito, Masahiro ^a,b   Matsuo, Yo ^c   Nishikawa, Ken ^b  

^a JAPAN ADVANCED INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

^c FuLaboratories Ltd   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE;

ALGORITHMS; ANIMALS; COMPUTERS; DATABASES, FACTUAL; EVALUATION STUDIES; HUMANS; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 0030774720     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/13.4.415     Document Type: Article

References (42)

1. Asai.K., Hyamizu.S. and Honda, K. (1993) Prediction of protein secondary structure by the hidden Markov model. Comput. Applic. Biosci., 9, 141-146.
2. Bauer.A. and Beyer.A. (1994) An improved pair potential to recognize native protein folds. Proteins Struct. Fund. Genet., 18, 254-261.
3. Bemstein, F.C. et al. (1977) A computer-based archival file for macromolecular structures. / Mol. Biol., 112, 535-542.
4. Bowie.J.U., Luthy, R. and Eisenberg.D. (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
5. Bryant, S.H. and Lawrence.C.E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins Struct. Fund. Genet., 16, 92-112.
6. Chou.P.Y. and Fasman.G.D. (1974) Prediction of protein conformation. Biochemistry, 13, 222-244.
7. Chou, P.Y. and Fasman, G.D. (1978) Prediction of the secondary structure of protein from their amino acid sequence. Adv. Enzymol.. 47, 45-148.
8. Di Francesco, V., Garnier, J. and Munson, P.J. (1996) improving protein secondary structure prediction with aligned homologous sequences. Protein Sci, 5, 106-113.
9. Frishman.D. and Argos.P. (1996) Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng., 9. 133-142.
10. Garnier, J., Osguthorpe, S.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.
11. Gibrat, J.F., Garnier, J. and Robson, B. (1987) Further development of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs. J. Mol. Biol., 198, 425-443.
12. Godzik.A., Kolinski.A. and Skolnick.J. (1992) Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol., 227, 227-238.
13. Goldstein.R.A., Luthey-Schlten.Z.A. and Wolynes.P.G. (1992) Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc. Natl Acad. Sci. USA. 89, 9029-9033.
14. Holley.L. and Karplus.M. (1989) Protein secondary structure prediction with a neural network. Proc. Natl Acad. Sci. USA, 86, 152-156.
15. Jones, D.T., Taylor.W.R. and ThorntonJ.M. (1992) A new approach to protein fold recognition. Nature, 358, 86-89.
16. Kabsch.W. and Sander.C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers, 22, 2577-2637.
17. Kneller.D.G., Cohen.F.E. and Langridge.R. (1990) Improvements in protein secondary structure prediction by an enhanced neural network. J. Mol. Biol., 214, 171-182.
18. KocherJ.A., Rooman.MJ. and Wodak.SJ. (1994) Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol., 235, 1598-1613.
19. Kyte, J. and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
20. Levin, J.M and Garnier, J. (1988) Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool. Biochim. Biophys. Ada, 955, 283-295.
21. Maiorov.V.N. and Crippen.G.M. (1992) Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol., 227, 876-888.
22. Matsuo.Y. and Nishikawa.K. (1994) Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci., 3, 2055-2063.
23. Matsuo.Y. and Nishikawa.K. (1995) Assessment of a protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding and local conformation. Proteins Struct. Fund. Genet., 23, 370-375.
24. Matsuo.Y., Nakamura.H. and Nishikawa.K. (1995) Detection of protein 3D-1D compatibility characterized by the evaluation of side-chain packing and electrostatic interactions. J. Biochem. (Tokyo), 118, 137-148.
25. Matthews.B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Ada, 405, 442-451.
26. Mehta, P.K., Heringa, J. and Argos, P. (1995) A simple and fast approach to prediction of protein secondary structure from multiply aligned sequences with accuracy above 70%. Protein Sci., 4, 2517-2525.
27. Muggleton.S., King.R.D. and Sternberg.MJ.E. (1992) Protein secondary structure prediction using logic based machine learning. Protein Eng., 5, 647-657.
28. Murzin.A.G., Brenner.S.E., Tubbard.T. and Chothia.C. (1995) SCOP: a structural classification of protein database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
29. Nishikawa.K. and Matsuo.Y. (1993) Development of pseudoenergy potentials for assessing protein 3D-ID compatibility and detecting weak homologies. Protein Eng., 6, 811-820.
30. Nishikawa.K. and Noguchi.T. (1991) Predicting protein secondary structure based on amino acid sequence. Methods Enzymol., 202. 31-44.
31. Nishikawa.K. and Ooi.T. (1986) Amino acid sequence homology applied to the prediction of protein secondary structures. Biochim. Biophys. Ada, 871, 45-54.
32. Ouzounis.C. Sander.C., Scharf.M. and Schneider.RJ. (1993) Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures. J. Mol. Biol., 232, 805-825.
33. Qian.N. and Sejnowski.T.J. (1988) Prediction of the secondary structure of globular proteins using neural network. J. Mol. Biol., 202, 865-884.
34. Rost.B. and Sander.C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
35. Salamov.A.A. and Solovyev.V.V. (1995) Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. J. Mol. Biol., 247, 11-15.
36. Salzberg.S. and Cost.S. (1992) Predicting protein secondary structure with a nearest-neighbor algorithm. J. Mol. Biol., 227, 371-374.
37. Sippl.M.J. (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol, 213. 859-883.
38. Wako.H. and Blundell.T.L. (1994) Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structure. J. Mol. Biol., 238, 693-708.
39. Wilmanns.M. and Eisenberg.D. (1993) Three-dimensional profiles from residue-pair preferences: identification of sequences with a/β-barrel fold. Proc. NatlAcad. Sci. USA, 90, 1379-1383.
40. Yi, T.-M. and Lander.E.S. (1993) Protein secondary structure prediction using nearest-neighbor methods. J. Mol. Biol., 232. 1117-1129.
41. Zhang, X., Merirov.J.P. and Waltz.D.L. (1992) Hybrid system for protein secondary structure prediction. J. Mol. Biol., 225, 1049-1063.
42. Zvelebil.M.J., Barton.G.J., Taylor.W.R. and Stemberg.M.J. (1987) Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol., 195, 957-961.