Protein contact order prediction from primary sequences

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Shi, Yi ^a   Zhou, Jianjun ^a   Arndt, David ^a   Wishart, David S ^a   Lin, Gouhui ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID COMPOSITIONS; CORRELATION COEFFICIENT; NUMBER OF COMPONENTS; PROTEIN FOLDING RATES; PROTEIN STRUCTURE PREDICTION; SECONDARY STRUCTURES; THREE-DIMENSIONAL STRUCTURE; WEIGHTED LINEAR COMBINATIONS;

AMINO ACIDS; FORECASTING; PROTEIN FOLDING; THREE DIMENSIONAL;

PROTEINS;

ALPHA HELIX; AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; CORRELATION COEFFICIENT; INTERNET; PREDICTION; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; ALGORITHM; BINDING SITE; CHEMISTRY; METHODOLOGY; MOLECULAR GENETICS; PROTEIN BINDING;

PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 46149100783     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-255     Document Type: Article

References (41)

1. Kim PS Baldwin RL Intermediates in the folding reactions of small proteins Annual Review of Biochemistry 1990, 59:631-660. 2197986 10.1146/ annurev.bi.59.070190.003215
2. Kubelka J Hofrichter J Eaton WA The protein folding "speed limit" Curr Opin Struct Biol 2004, 14:76-88. 15102453 10.1016/ j.sbi.2004.01.013
3. Tanaka S Scheraga HA Model of protein folding: inclusion of short-, medium-, and long-range interactions Proc Natl Acad Sci U S A 1975, 72:3802-3806. 1060065 10.1073/pnas.72.10.3802 433083
4. Fezoui Y Braswell EH Xian W Osterhout JJ Dissection of the de novo designed peptide alpha-t-alpha: stability and properties of the intact molecule and its constituent helices Biochemistry 1999, 38:2796-2804. 10052951 10.1021/bi9823838
5. Kabsch W Sander C Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22:2577-2637. 6667333 10.1002/bip.360221211
6. Plaxco KW Simons KT Baker D Contact order, transition state placement and the refolding rates of single domain proteins J Mol Biol 1998, 277:985-994. 9545386 10.1006/jmbi.1998.1645
7. Lee B Richards FM The interpretation of protein structures: Estimation of static accessibility Journal of Molecular Biology 1971, 55:379-380. 5551392 10.1016/0022-2836(71)90324-X
8. Alm E Baker D Matching theory and experiment in protein folding Current Opinion in Structural Biology 1999, 9:189-196. 10322214 10.1016/ S0959-440X(99)80027-X
9. Grantcharova V Alm EJ Baker D Horwich AL Mechanisms of protein folding Current Opinion in Structural Biology 2001, 11:70-82. 11179895 10.1016/ S0959-440X(00)00176-7
10. Bonneau R Ruczinski I Tsai J Baker D Contact order and ab initio protein structure prediction Protein Science 2002, 11:1937-1944. 12142448 10.1110/ps.3790102 2373674
11. Ivankov DN Garbuzynskiy SO Alm E Plaxco KW Baker D Finkelstein AV Contact order revisited: Influence of protein size on the folding rate Protein Sci 2003, 12:2057-2062. 12931003 10.1110/ps.0302503 2324001
12. Baker D A surprising simplicity to protein folding Nature 2000, 405:39-42. 10811210 10.1038/35011000
13. Koga N Takada S Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model Journal of Molecular Biology 2001, 313:171-180. 11601854 10.1006/jmbi.2001.5037
14. Ivankov DN Finkelstein AV Prediction of protein folding rates from the amino acid sequence-predicted secondary structure Proceedings of the National Academy of Sciences of the USA 2004, 101:8942-8944. 15184682 10.1073/pnas.0402659101 428451
15. Gromiha MM Thangakani AM Selvaraj S FOLD-RATE: prediction of protein folding rates from amino acid sequence Nucleic Acids Research 2006, 34:W70-W74. 16845101 10.1093/nar/gkl043 1538837
16. Gromiha MM Selvaraj S Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction Journal of Molecular Biology 2001, 310:27-32. 11419934 10.1006/jmbi.2001.4775
17. Chivian D Kim DE Malmstrom L Schonbrun J Rohl CA Baker D Prediction of CASP6 structures using automated Robetta protocols Website 2005. http://robetta.bakerlab.org/pub/dylan/
18. Yuan Z Better prediction of protein contact number using a support vector regression analysis of amino acid sequence BMC Bioinformatics 2005, 6:248. 16221309 10.1186/1471-2105-6-248 1277819
19. Kinjo AR Nishikawa K Predicting secondary structures, contact numbers, and residue-wise contact orders of native protein structure from amino acid sequence using critical random networks Biophysics 2005, 1:67-74. 10.2142/biophysics.1.67
20. Kihara D On the effect of long range interactions on secondary structure formation in proteins Protein Science 2005, 14:1955-1963. 15987894 10.1110/ps.051479505 2279307
21. Kinjo AR Nishikawa K CRNPRED: highly accurate prediction of one-dimensional protein structures by large-scale critical random networks BMC Bioinformatics 2006, 7:401. 16952323 10.1186/ 1471-2105-7-401 1578593
22. Song J Burrage K Predicting residue-wise contact orders in proteins by support vector regression BMC Bioinformatics 2006, 7:425. 17014735 10.1186/1471-2105-7-425 1618864
23. Kinjo AR Nishikawa K Recoverable one-dimensional encoding of three-dimensional protein structures Bioinformatics 2005, 21:2167-2170. 15722374 10.1093/bioinformatics/bti330
24. Kinjo AR Horimoto K Nishikawa K Predicting absolute contact numbers of native protein structure from amino acid sequence Proteins 2005, 58:158-165. 15523668 10.1002/prot.20300
25. Fariselli P Casadio R RCNPRED: prediction of the residue co-ordination numbers in proteins Bioinformatics 2001, 17:202-204. 11238082 10.1093/ bioinformatics/17.2.202
26. Pollastri G Baldi P Fariselli P Casadio R Improved prediction of the number of residue contacts in proteins by recurrent neural networks Bioinformatics 2001, 17:S234-S242. 11473014
27. Pollastri G Baldi P Fariselli P Casadio R Prediction of coordination number and relative solvent accessibility in proteins Proteins 2002, 47:142-153. 11933061 10.1002/prot.10069
28. Ishida T Nakamura S Shimizu K Potential for assessing quality of protein structure based on contact number prediction Proteins 2006, 64:940-947. 16788993 10.1002/prot.21047
29. Mitchell T Machine Learning McGraw Hill 1997.
30. Calculate the Contact Order of Proteins http://depts.washington.edu/ bakerpg/contact_order/
31. Montgomerie S Sundararaj S Gallin W Wishart DS Improving the accuracy of protein secondary structure prediction using structural alignment BMC Bioinformatics 2006, 7:301. 16774686 10.1186/1471-2105-7-301 1550433
32. Wang G Dunbrack RL Jr PISCES: a protein sequence culling server Bioinformatics 2003, 19:1589-1591. 12912846 10.1093/bioinformatics/btg224
33. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool Journal of Molecular Biology 1990, 215:403-410. 2231712
34. Willard L Ranjan A Zhang H Monzavi H Boyko RF Sykes BD Wishart DS VADAR: a web server for quantitative evaluation of protein structure quality Nucleic Acids Research 2003, 31:3316-3319. 12824316 10.1093/nar/gkg565 168972
35. Wishart DS Arndt D Berjanskii M Guo AC Shi Y Shrivastava S Zhou J Zhu Y Lin GH PPT-DB: The Protein Property Prediction and Testing Database Nucleic Acids Research 2008, 36:D222-D229. 17916570 10.1093/nar/gkm800 2238980
36. Smola AJ Schölkopf B A tutorial on support vector regression Statistics and Computing 2003, 14:199-222. 10.1023/ B:STCO.0000035301.49549.88
37. Anderson JA An Introduction to Neural Networks MIT Press 1995.
38. Protein Contact Order Prediction/Calculation Web Sever http://www.copredictor.ca
39. Berman HM Westbrook J Feng Z Gilliland G Bhat TN Weissig H Shindyalov IN Bourne PE The Protein Data Bank Nucleic Acids Research 2000, 28:235-242. 10592235 10.1093/nar/28.1.235 102472
40. Andreeva A Howorth D Brenner SE Hubbard TJP Chothia C Murzin AG SCOP database in 2004: refinements integrate structure and sequence family data Nucleic Acids Research 2004, 32:D226-D229. 14681400 10.1093/nar/ gkh039 308773
41. Shindyalov IN Bourne PE Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Engineering 1998, 11:739-747. 9796821 10.1093/protein/11.9.739