Biomedical Engineering Reference
In-Depth Information
23. Pasquier C, Promponas VJ, Palaios GA, Hamodrakas JS, Hamodrakas SJ (1999) A novel
method for predicting transmembrane segments in proteins based on a statistical analysis of
the SwissProt database: the PRED-TMR algorithm. Protein Eng 12:381-385
24. Kitsas IK, Hadjileontiadis LJ, Panas SM (2008) Transmembrane helix prediction in proteins
using hydrophobicity properties and higher-order statistics. Comp Biol Med 38:867-880
25. Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J (2008) Transmembrane
helix prediction using amino acid property features and latent semantic analysis. BMC
Bioinform 9:S4
26. Tusnady GE, Simon I (1998) Principles governing amino acid composition of integral
membrane proteins: application to topology prediction. J Mol Biol 283:489-506
27. Rost B, Sander C, Casadio R, Fariselli P (1995) Transmembrane helices predicted at 95%
accuracy. Protein Sci 4:521-533
28. Jones DT, Taylor WR, Thornton JM (1994) A model recognition approach to the prediction of
all-helical membrane protein structure and topology. Biochemistry 33:3038-3049
29. Persson B, Argos P (1996) Topology prediction of membrane proteins. Protein Sci 5:363-371
30. Liu JF, Rost B (2001) Comparing function and structure between entire proteomes. Protein Sci
10:1970-1979
31. Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A (1997) Prediction of transmembrane
alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein
Eng 10:673-676
32. Nugent T, Jones DT (2009) Transmembrane protein topology prediction using support vector
machines. BMC Bioinform 10:159
33. Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK (2010) Active machine
learning for transmembrane helix prediction. BMC Bioinform 11:S58
34. Ahmed R, Rangwala H, Karypis G (2010) TOPTMH: topology predictor for transmembrane
alpha-helices. J Bioinform Comput Biol 8:39-57
35. Park Y, Helms V (2006) Assembly of transmembrane helices of simple polytopic membrane
proteins from sequence conservation patterns. Proteins Struct Funct Bioinf 64:895-905
36. Fuchs A, Kirschner A, Frishman D (2009) Prediction of helix-helix contacts and interacting
helices in polytopic membrane proteins using neural networks. Proteins Struct Funct Bioinf
74:857-871
37. Michino M, Chen JH, Stevens RC, Brooks CL (2010) FoldGPCR: structure prediction protocol
for the transmembrane domain of G protein-coupled receptors from class A. Proteins Struct
Funct Bioinf 78:2189-2201
38. de Brevern AG (2010) 3D structural models of transmembrane proteins. Meth Mol Biol
654:387-401
39. Schulz GE (2000) beta-Barrel membrane proteins. Curr Opin Struct Biol 10:443-447
40. Gnanasekaran TV, Peri S, Arockiasamy A, Krishnaswamy S (2000) Profiles from structure
based sequence alignment of porins can identify beta stranded integral membrane proteins.
Bioinformatics 16:839-842
41. Wimley WC (2002) Toward genomic identification of beta-barrel membrane proteins: com-
position and architecture of known structures. Protein Sci 11:301-312
42. Liu Q, Zhu YS, Wang BH, Li YX (2003) Identification of beta-barrel membrane proteins based
on amino acid composition properties and predicted secondary structure. Comp Biol Chem
27:355-361
43. Gromiha MM, Suwa M (2005) A simple statistical method for discriminating outer membrane
proteins with better accuracy. Bioinformatics 21:961-968
44. Gromiha MM, Ahmad S, Suwa M (2005) Application of residue distribution along the
sequence for discriminating outer membrane proteins. Comp Biol Chem 29:135-142
45. Gromiha MM (2005) Motifs in outer membrane protein sequences: applications for discrimi-
nation. Biophys Chem 117:65-71
46. Rost B, Sander C (1993) Prediction of protein secondary structure at better than 70% accuracy.
J Mol Biol 232:584-599
