TMBpro: Secondary structure, β-contact and tertiary structure prediction of transmembrane β-barrel proteins

Bioinformatics

Volumn 24, Issue 4, 2008, Pages 513-520

  Randall, Arlo ^a,b   Cheng, Jianlin ^c   Sweredoski, Michael ^a,b   Baldi, Pierre ^a,b  

^a Ringgold Standard Institution Informatics   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN;

ACCURACY; ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; COMPUTER PREDICTION; CONTROLLED STUDY; CORRELATION COEFFICIENT; INTERMETHOD COMPARISON; PERFORMANCE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; QUALITY CONTROL; VALIDATION PROCESS;

NEGIBACTERIA;

EID: 39149140433     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm548     Document Type: Article

References (52)

1. Altschul,S. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids: Res. 25, 3389-3402.
2. Bagos.P. et al. (2004a) A hidden markov model method, capable of predicting and discriminating beta-barrel outer membrane proteins. BMC Bioinformatics, 5, 29.
3. Hagos,P. et al. (2004b) PRED-TMBB: A web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res. 32, W400-W404.
4. Bagos,P. et al. (2005) Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method. BMC Bioinformatics, 6, 7.
5. Baldi,P. et al. (2000) Assessing the accuracy of prediction algorithms for classification: An overview. Bioinformatics, 16 412-424.
6. Baldi,P. and Pollastri,G. (2003) The principled design of large-scale recursive neuralnetwork architectures-DAG-RNNs and the protein structure prediction problem. J. Mach. Learn. Res., 4, 575-602.
7. Berman,H. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
8. Bigelow,H. and Rost,B. (2006) PROFtmb: A web server for predicting bacterial transmembrane beta barrel proteins. Nucleic Acids Res., 34, W186-W188.
9. Bigelow,H. et al. (2004) Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res., 32, 2566-2577.
10. Casadio,R. et al. (2003) In silico prediction of the structure of membrane proteins: Is it feasible? Brief. Bioinformatics, 4, 341-348.
11. Cheng,J. and Baldi,P. (2005) Three-stage prediction of protein beta-sheets by neural networks, alignments, and graph algorithms. Bioinformatics, 21 (Suppl. 1), i75-i84.
12. Cheng,J. et al. (2005) Accurate prediction of protein disordered regions by mining protein structure data. Data Mining Knowl. Discov. 11, 213-222.
13. Cheng,J. et al. (2006a) Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins, 62, 617-629.
14. Cheng,J. et al. (2006b) DOMpro: Protein domain prediction using profiles, secondary structure, relative solvent accessibility, and recursive neural networks. Data Mining Knowl. Discov., 13, 1-10.
15. Diederichs,K. et al. (1998) Prediction by a neural network of outer membrane beta-strand protein topology. Protein Sci., 7 2413-2420.
16. Fariselli,P. et al. (2005) A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Boinformatics, 6, S12.
17. Garrow,A. et al. (2005) TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics, 6, 56.
18. Gromiha,M. and Suwa,M. (2005) A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics, 21, 961-968.
19. Gromiha,M. et al. (1997) Identification of membrane spanning beta strands in bacterial porins. Protein Eng., 10, 497-500.
20. Gromiha,M. et al. (2004) Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. J. Comput. Chem., 25, 762-767.
21. Gromiha,M. et al. (2005) TMBETA-NET: Discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. Nucleic Acids Res., 33, W164-W167.
22. Ikeda,M. et al. (2003) TMPDB: A database of experimentally-characterized transmembrane topologies. Nucleic Acids Res., 31, 406-409.
23. Jackups,R. and Liang,J. (2005) Interstrand pairing patterns in beta-barrel membrane proteins: The positive-outside rule, aromatic rescue, and strand registration-prediction. J. Mol. Biol., 354 979-993.
24. Jacoboni,I. et al. (2001) Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network based predictor. Protein Sci., 10, 779-787.
25. Kabsch,W. and Sander,C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
26. Koebnik,R. et al. (2000) Structure and function of bacterial outer membrane proteins: Barrels in a nutshell. Mol. Microbiol., 37 239-253.
27. Liu,Q. et al. (2003) A HMM-based method to predict the transmembrane regions of beta-barrel membrane proteins. Comput. Biol. Chem., 27, 60-76.
28. Lomize,M. et al. (2006) OPM: Orientations of proteins in membrane database. Bioinformatics, 22, 623-625.
29. Martelli,P. et al. (2002) A sequence-profile-based hmm for predicting and discriminating beta barrel membrane proteins. Bioinformatics, 18, S46-S53.
30. Moult,J. et al. (2005) Critical assessment of methods of protein structure prediction (CASP) - Round 6. Proteins, 61 (Suppl. 7), 3-7.
31. Natt,N. et al. (2004) Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods. Proteins, 56, 11-18.
32. Oberai,A. et al. (2006) A limited universe of membrane protein families and folds. Protein Sci., 15, 1723-1734.
33. Park,K. et al. (2005) Discrimination of outer membrane proteins using support vector machines. Bioinformatics, 21, 4223-4229.
34. Paul,C. and Rosenbusch,J. (1985) Folding patterns of porin and bacteriorhodopsin. EMBO J., 4, 1593-1597.
35. Pollastri,G. and Baldi,P. (2002) Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics, 18, S62-S70.
36. Pollastri,G. et al. (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins, 47, 228-235.
37. Schulz,G. (2000) Beta-barrel membrane proteins. Curr. Opin. Struct. Biol., 10, 443-447.
38. Simons,K.T. et al. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
39. Skolnick,J. et al. (1997) Monsster: A method for folding globular proteins with a small number of distance restraints. J. Mol. Biol. 265, 217-241.
40. Tamm,L. et al. (2001) Structure and assembly of beta-barrel membrane proteins. J. Biol. Chem., 276, 32399-32402.
41. Tamm,L. et al. (2004) Folding and assembly of beta barrel membrane proteins. Biochim. Biophys. Acta, 1666, 250-263.
42. Waldispühl,J. et al. (2006a) Predicting transmembrane beta-barrels and interstrand residue interactions from sequence. Proteins, 65, 61-74.
43. Waldispühl,J. et al. (2006b) transFold: A web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res., 34, W189-W193.
44. Wallin,E. and von Heijne,G. (1998) Genome wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci., 7, 1029-1038.
45. Welte,W. et al. (1991) Prediction of the general structure of OmpF and PhoE from the sequence and structure of porin from Rhodobacter capsulatus. Orientation of porin in the membrane. Biochim. Biophys. Acta, 1080, 271-274.
46. Wimley,W. (2002) Toward genomic identification of beta-barrel membrane proteins:cOmposition and architecture of known structures. Protein Sci., 11, 301-312.
47. Wimley,W. (2003) The versatile beta-barrel membrane protein. Curr. Opin. Struct. Biol., 13, 404-411.
48. Yooseph,S. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 5, e16.
49. Zemla,A. et al. (1999) A modified definition of sov, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223.
50. Zemla,A. (2003) LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res., 31, 3370-3374.
51. Zhai,Y. and Saier,M. (2002) The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci., 11, 2196-2207.
52. Zhang,T. et al. (2003) TOUCHSTONE:II a new approach to ab initio protein structure prediction. Biophys. J., 85, 1145-1164.