Outer membrane proteins can be simply identified using secondary structure element alignment

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Yan, Ren Xiang ^a   Chen, Zhen ^a   Zhang, Ziding ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK EXPERIMENTS; GLOBULAR PROTEINS; GRAM-NEGATIVE BACTERIA; MEMBRANE PROTEINS; OUTER MEMBRANE PROTEIN; PREDICTION PERFORMANCE; SECONDARY STRUCTURE ELEMENTS; SECONDARY STRUCTURES;

ALIGNMENT; BENCHMARKING; BIOLOGICAL MEMBRANES;

PROTEINS;

NEGIBACTERIA;

ESCHERICHIA COLI PROTEIN; MEMBRANE PROTEIN; OUTER MEMBRANE PROTEIN;

ARTICLE; CHEMISTRY; GENETICS; METHODOLOGY; PROTEIN SECONDARY STRUCTURE; PROTEOMICS;

BACTERIAL OUTER MEMBRANE PROTEINS; ESCHERICHIA COLI PROTEINS; MEMBRANE PROTEINS; PROTEIN STRUCTURE, SECONDARY; PROTEOMICS;

EID: 79952703533     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-76     Document Type: Article

References (51)

1. Gromiha MM, Ahmad S, Suwa M. Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput Biol Chem 2005, 29(2):135-142. 10.1016/j.compbiolchem.2005.02.006, 15833441.
2. Berven FS, Flikka K, Jensen HB, Eidhammer I. BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res 2004, (32 Web Server):W394-399. 10.1093/nar/gkh351, 441489, 15215418.
3. Garrow AG, Westhead DR. A consensus algorithm to screen genomes for novel families of transmembrane beta barrel proteins. Proteins 2007, 69(1):8-18. 10.1002/prot.21439, 17557332.
4. Wu Z, Feng E, Wang Y, Chen L. Discrimination of outer membrane proteins by a new measure of information discrepancy. Protein Pept Lett 2007, 14(1):37-44. 10.2174/092986607779117254, 17266649.
5. Gromiha MM, Suwa M. Discrimination of outer membrane proteins using machine learning algorithms. Proteins 2006, 63(4):1031-1037. 10.1002/prot.20929, 16493651.
6. Park KJ, Gromiha MM, Horton P, Suwa M. Discrimination of outer membrane proteins using support vector machines. Bioinformatics 2005, 21(23):4223-4229. 10.1093/bioinformatics/bti697, 16204348.
7. Remmert M, Linke D, Lupas AN, Soding J. HHomp--prediction and classification of outer membrane proteins. Nucleic Acids Res 2009, (37 Web Server):W446-451. 10.1093/nar/gkp325, 2703889, 19429691.
8. Liu Q, Zhu Y, Wang B, Li Y. Identification of beta-barrel membrane proteins based on amino acid composition properties and predicted secondary structure. Comput Biol Chem 2003, 27(3):355-361. 10.1016/S1476-9271(02)00085-3, 12927109.
9. Gromiha MM, Majumdar R, Ponnuswamy PK. Identification of membrane spanning beta strands in bacterial porins. Protein Eng 1997, 10(5):497-500. 10.1093/protein/10.5.497, 9215567.
10. Lin H. The modified Mahalanobis Discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition. J Theor Biol 2008, 252(2):350-356. 10.1016/j.jtbi.2008.02.004, 18355838.
11. Gromiha MM. Motifs in outer membrane protein sequences: applications for discrimination. Biophys Chem 2005, 117(1):65-71. 10.1016/j.bpc.2005.04.005, 15905018.
12. Gnanasekaran TV, Peri S, Arockiasamy A, Krishnaswamy S. Profiles from structure based sequence alignment of porins can identify beta stranded integral membrane proteins. Bioinformatics 2000, 16(9):839-842. 10.1093/bioinformatics/16.9.839, 11108707.
13. Bigelow H, Rost B. PROFtmb: a web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res 2006, (34 Web Server):W186-188. 10.1093/nar/gkl262, 1538807, 16844988.
14. Martelli PL, Fariselli P, Krogh A, Casadio R. A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 2002, 18(Suppl 1):S46-53.
15. Gromiha MM, Suwa M. A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 2005, 21(7):961-968. 10.1093/bioinformatics/bti126, 15531602.
16. Garrow AG, Agnew A, Westhead DR. TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res 2005, (33 Web Server):W188-192. 10.1093/nar/gki384, 1160145, 15980452.
17. Yan C, Hu J, Wang Y. Discrimination of outer membrane proteins with improved performance. BMC Bioinformatics 2008, 9:47. 10.1186/1471-2105-9-47, 2254589, 18218108.
18. Wimley WC. Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci 2002, 11(2):301-312. 10.1110/ps.29402, 2373429, 11790840.
19. Zhai Y, Saier MH. The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci 2002, 11(9):2196-2207. 10.1110/ps.0209002, 2373602, 12192075.
20. Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics 2004, 5:29. 10.1186/1471-2105-5-29, 385222, 15070403.
21. Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ. PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res 2004, (32 Web Server):W400-404. 10.1093/nar/gkh417, 441555, 15215419.
22. Natt NK, Kaur H, Raghava GP. Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. Proteins 2004, 56(1):11-18. 10.1002/prot.20092, 15162482.
23. Gromiha MM, Ahmad S, Suwa M. TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res 2005, (33 Web Server):W164-167. 10.1093/nar/gki367, 1160128, 15980447.
24. Freeman TC, Wimley WC. A highly accurate statistical approach for the prediction of transmembrane beta-barrels. Bioinformatics 26(16):1965-1974. 10.1093/bioinformatics/btq308, 20538726.
25. Yan C, Hu J, Wang Y. Discrimination of outer membrane proteins using a K-nearest neighbor method. Amino Acids 2008, 35(1):65-73. 10.1007/s00726-007-0628-7, 18219549.
26. Deng Y, Liu Q, Li YX. Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem 2004, 28(3):189-194. 10.1016/j.compbiolchem.2004.02.004, 15261149.
27. Bagos PG, Liakopoulos TD, Hamodrakas SJ. Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics 2005, 6:7. 10.1186/1471-2105-6-7, 545999, 15647112.
28. Koebnik R, Locher KP, Van Gelder P. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol 2000, 37(2):239-253. 10.1046/j.1365-2958.2000.01983.x, 10931321.
29. Garrow AG, Agnew A, Westhead DR. TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics 2005, 6:56. 10.1186/1471-2105-6-56, 1274253, 15769290.
30. Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B. Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res 2004, 32(8):2566-2577. 10.1093/nar/gkh580, 419468, 15141026.
31. Przytycka T, Aurora R, Rose GD. A protein taxonomy based on secondary structure. Nat Struct Biol 1999, 6(7):672-682. 10.1038/10728, 10404226.
32. Bindewald E, Cestaro A, Hesser J, Heiler M, Tosatto SC. MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification. Protein Eng 2003, 16(11):785-789. 10.1093/protein/gzg106, 14631066.
33. Lobley A, Sadowski MI, Jones DT. pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics 2009, 25(14):1761-1767. 10.1093/bioinformatics/btp302, 19429599.
34. McGuffin LJ, Jones DT. Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 2003, 19(7):874-881. 10.1093/bioinformatics/btg097, 12724298.
35. Zhang Z, Kochhar S, Grigorov MG. Descriptor-based protein remote homology identification. Protein Sci 2005, 14(2):431-444. 10.1110/ps.041035505, 2253398, 15632283.
36. Yan RX, Si JN, Wang C, Zhang Z. DescFold: a web server for protein fold recognition. BMC Bioinformatics 2009, 10:416. 10.1186/1471-2105-10-416, 2803855, 20003426.
37. McGuffin LJ, Jones DT. Targeting novel folds for structural genomics. Proteins 2002, 48(1):44-52. 10.1002/prot.10129, 12012336.
38. Si JN, Yan RX, Wang C, Zhang Z, Su XD. TIM-Finder: A new method for identifying TIM-barrel proteins. BMC Struct Biol 2009, 9(1):73. 10.1186/1472-6807-9-73, 2803183, 20003393.
39. Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SC. The SSEA server for protein secondary structure alignment. Bioinformatics 2005, 21(3):393-395. 10.1093/bioinformatics/bti013, 15347578.
40. Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970, 48(3):443-453. 10.1016/0022-2836(70)90057-4, 5420325.
41. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292(2):195-202. 10.1006/jmbi.1999.3091, 10493868.
42. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
43. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22(13):1658-1659. 10.1093/bioinformatics/btl158, 16731699.
44. Rychlewski L, Fischer D. LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. Protein Sci 2005, 14(1):240-245. 10.1110/ps.04888805, 2253323, 15608124.
45. Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 2001, 17(12):1242-1243. 10.1093/bioinformatics/17.12.1242, 11751240.
46. Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FS. PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Res 2005, (33 Database):D164-168. 539981, 15608169.
47. Tsirigos KD, Bagos PG, Hamodrakas SJ. OMPdb: a database of {beta}-barrel outer membrane proteins from Gram-negative bacteria. Nucleic Acids Res 3013764, 20952406.
48. Wimley WC. The versatile beta-barrel membrane protein. Curr Opin Struct Biol 2003, 13(4):404-411. 10.1016/S0959-440X(03)00099-X, 12948769.
49. Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340(4):783-795. 10.1016/j.jmb.2004.05.028, 15223320.
50. Ren Q, Kang KH, Paulsen IT. TransportDB: a relational database of cellular membrane transport systems. Nucleic Acids Res 2004, (32 Database):D284-288. 10.1093/nar/gkh016, 308751, 14681414.
51. Andreeva A, Howorth D, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res 2004, (32 Database):D226-229. 10.1093/nar/gkh039, 308773, 14681400.