The relationship between N-gram patterns and protein secondary structure

Proteins: Structure, Function and Genetics

Volumn 68, Issue 4, 2007, Pages 830-838

  Vries, John K ^a   Liu, Xiong ^a,b   Bahar, Ivet ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

n gram patterns; Protein sequence analysis; Secondary structure; Structural bioinformatics

Indexed keywords

AMINO ACID;

ACCURACY; ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CLASSIFICATION ALGORITHM; JACKKNIFE TEST; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; AMINO ACIDS; DATABASES, PROTEIN; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NANOTECHNOLOGY; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 34548752832     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21480     Document Type: Article

References (35)

1. Pauling L, Corey RB, Branson HR. The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 1951;37:205-211.
2. Kendrew JC, Watson HC, Strandberg BE, Dickerson RE, Phillips DC, Shore VC. The amino-acid sequence X-ray methods, and its correlation with chemical data. Nature 1961;190:666-670.
3. Ptitsyn OB, Finkelstein AV. Theory of protein secondary structure and algorithm of its prediction. Biopolymers 1983;22:15-25.
4. Rost B. Rising accuracy of protein secondary structure prediction. In: Chasman D, editor. Protein structure determination, analysis, and modeling for drug discovery. New York: Dekker; 2005.
5. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
6. Liu Y, Carbonell J, Klein-Seetharaman J, Gopalakrishnan V.Context sensitive vocabulary and its application in protein secondary structure prediction. ACM International Conference on Research and Development in Information Retrieval; 2004.
7. Wu CH, Zhao S, Chen HL, Lo CJ, McLarty J. Motif identification neural design for rapid and sensitive protein family search. Comput Appl Biosci 1996;12:109-118.
8. Rost B, Sander C. Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol 1993;232:584-599.
9. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol 1987;195:957-961.
10. Pollastri G, McLysaght A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 2005;21:1719-1720.
11. Jones DT, Swindells MB. Getting the most from PSI-BLAST. Trends Biochem Sci 2002;27:161-164.
12. Kloczkowski A, Ting KL, Jernigan RL, Garnier J. Combining the GOR V algorithm with evolutionary information for protein secondary structure prediction from amino acid sequence. Proteins 2002;49:154-166.
13. Lin K, Simossis VA, Taylor WR, Heringa J. A simple and fast secondary structure prediction method using hidden neural networks. Bioinformatics 2005;21:152-159.
14. Przybylski D, Rost B. Alignments grow, secondary structure prediction improves. Proteins 2002;46:197-205.
15. Pollastri G, Przybylski D, Rost B, Baldi P. Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002;47:228-235.
16. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
17. Karplus K, Hu B. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 2001;17:713-720.
18. Karplus K, Katzman S, Shackleford G, Koeva M, Draper J, Barnes B, Soriano M, Hughey R. SAM-T04: what is new in protein-structure prediction for CASP6. Proteins 2005;61(Suppl 7):135-142.
19. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Grana O, Pazos F, Valencia A, Sali A, Rost B. EVA: evaluation of protein structure prediction servers. Nucleic Acids Res 2003;31:3311-3315.
20. Bystroff C, Baker D. Prediction of local structure in proteins using a library of sequence-structure motifs. J Mol Biol 1998;281:565-577.
21. Bystroff C, Shao Y. Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 2002;18(Suppl 1):S54-S61.
22. Kuznetsov IB, Rackovsky S. On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci 2003;12:2420-2433.
23. Gong H, Isom DG, Srinivasan R, Rose GD. Local secondary structure content predicts folding rates for simple, two-state proteins. J Mol Biol 2003;327:1149-1154.
24. Vries JK, Munshi R, Tobi D, Klein-Seetharaman J, Benos PV, Bahar I. A sequence alignment-independent method for protein classification. Appl Bioinformatics 2004;3:137-148.
25. Penel S, Morrison RG, Mortishire-Smith RJ, Doig AJ. Periodicity in alpha-helix lengths and C-capping preferences. J Mol Biol 1999;293:1211-1219.
26. Frishman D, Argos P. Knowledge-based protein secondary structure assignment. Proteins 1995;23:566-579.
27. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
28. Bornot A, de Brevern AG. Protein beta-turn assignments. Bioinformation 2006;1:153-155.
29. Lodish H, Berk A, Zipursky L, Matsudaira P, Baltimore D, Darnell J. Molecular cell biology. New York; W.H. Freeman; 2000.
30. Rost S, Fregin A, Hunerberg M, Bevans CG, Muller CR, Oldenburg J. Site-directed mutagenesis of coumarin-type anticoagulant-sensitive VKORC1: evidence that highly conserved amino acids define structural requirements for enzymatic activity and inhibition by warfarin. Thromb Haemost 2005;94:780-786.
31. Kabani M, Beckerich JM, Gaillardin C. Sls1p stimulates Sec63p-mediated activation of Kar2p in a conformation-dependent manner in the yeast endoplasmic reticulum. Mol Cell Biol 2000;20:6923-6934.
32. Shannon CE. A mathematical theory of communications. Bell Syst Tech J 1948;27:379-423.
33. Birzele F, Kramer S. A new representation for protein secondary structure prediction based on frequent patterns. Bioinformatics 2006;22:2628-2634.
34. Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005;15:586-592.
35. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.