-
1
-
-
0030759333
-
Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
-
Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A. Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng 1997;10(6):673-676.
-
(1997)
Protein Eng
, vol.10
, Issue.6
, pp. 673-676
-
-
Cserzo, M.1
Wallin, E.2
Simon, I.3
Von Heijne, G.4
Elofsson, A.5
-
2
-
-
2642587355
-
Prediction of transmembrane regions of beta-barrel proteins using ANN- and SVM-based methods
-
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.
-
(2004)
Proteins
, vol.56
, Issue.1
, pp. 11-18
-
-
Natt, N.K.1
Kaur, H.2
Raghava, G.P.3
-
3
-
-
4944242989
-
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
-
Martelli PL, Fariselli P, Casadio R. An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics 2003;19(Suppl 1):i205-211.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Martelli, P.L.1
Fariselli, P.2
Casadio, R.3
-
4
-
-
2942624227
-
Advances in the prediction of protein targeting signals
-
Schneider G, Fechner U. Advances in the prediction of protein targeting signals. Proteomics 2004;4(6):1571-1580.
-
(2004)
Proteomics
, vol.4
, Issue.6
, pp. 1571-1580
-
-
Schneider, G.1
Fechner, U.2
-
5
-
-
0033044637
-
Machine learning approaches for the prediction of signal peptides and other protein sorting signals
-
Nielsen H, Brunak S, von Heijne G. Machine learning approaches for the prediction of signal peptides and other protein sorting signals. Protein Eng 1999;12(1):3-9.
-
(1999)
Protein Eng
, vol.12
, Issue.1
, pp. 3-9
-
-
Nielsen, H.1
Brunak, S.2
Von Heijne, G.3
-
6
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
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.
-
(2004)
J Mol Biol
, vol.340
, Issue.4
, pp. 783-795
-
-
Bendtsen, J.D.1
Nielsen, H.2
Von Heijne, G.3
Brunak, S.4
-
7
-
-
0030614959
-
Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
-
Nielsen H, Engelbrecht J, Brunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 1997;10(1):1-6.
-
(1997)
Protein Eng
, vol.10
, Issue.1
, pp. 1-6
-
-
Nielsen, H.1
Engelbrecht, J.2
Brunak, S.3
Von Heijne, G.4
-
8
-
-
0034697980
-
Predicting subcellular localization of proteins based on their N-terminal amino acid sequence
-
Emanuelsson O, Nielsen H, Brunak S, von Heijne G. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000;300(4):1005-1016.
-
(2000)
J Mol Biol
, vol.300
, Issue.4
, pp. 1005-1016
-
-
Emanuelsson, O.1
Nielsen, H.2
Brunak, S.3
Von Heijne, G.4
-
9
-
-
0344118117
-
Better prediction of sub-cellular localization by combining evolutionary and structural information
-
Nair R, Rost B. Better prediction of sub-cellular localization by combining evolutionary and structural information. Proteins 2003;53(4):917-930.
-
(2003)
Proteins
, vol.53
, Issue.4
, pp. 917-930
-
-
Nair, R.1
Rost, B.2
-
10
-
-
3242877807
-
ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST
-
Bhasin M, Raghava GP. ESLpred: SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST. Nucleic Acids Res 2004;32(Web Server issue):W414-419.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Bhasin, M.1
Raghava, G.P.2
-
11
-
-
1542400030
-
Predicting subcellular localization of proteins using machine-learned classifiers
-
Lu Z, Szafron D, Greiner R, et al. Predicting subcellular localization of proteins using machine-learned classifiers. Bioinformatics 2004;20(4):547-556.
-
(2004)
Bioinformatics
, vol.20
, Issue.4
, pp. 547-556
-
-
Lu, Z.1
Szafron, D.2
Greiner, R.3
-
12
-
-
3242891478
-
LOCnet and LOCtarget: Sub-cellular localization for structural genomics targets
-
Nair R, Rost B. LOCnet and LOCtarget: sub-cellular localization for structural genomics targets. Nucleic Acids Res 2004;32(Web Server issue):W517-521.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Nair, R.1
Rost, B.2
-
13
-
-
2942513121
-
Esub8: A novel tool to predict protein subcellular localizations in eukaryotic organisms
-
Cui Q, Jiang T, Liu B, Ma S. Esub8: a novel tool to predict protein subcellular localizations in eukaryotic organisms. BMC Bioinformatics 2004;5(1):66.
-
(2004)
BMC Bioinformatics
, vol.5
, Issue.1
, pp. 66
-
-
Cui, Q.1
Jiang, T.2
Liu, B.3
Ma, S.4
-
14
-
-
0036459850
-
An overview on predicting the subcellular location of a protein
-
Feng ZP. An overview on predicting the subcellular location of a protein. In Silico Biol 2002;2(3):291-303.
-
(2002)
In Silico Biol
, vol.2
, Issue.3
, pp. 291-303
-
-
Feng, Z.P.1
-
15
-
-
1242274331
-
Prediction of RNA-binding proteins from primary sequence by a support vector machine approach
-
Han LY, Cai CZ, Lo SL, Chung MC, Chen YZ. Prediction of RNA-binding proteins from primary sequence by a support vector machine approach. RNA 2004;10(3):355-368.
-
(2004)
RNA
, vol.10
, Issue.3
, pp. 355-368
-
-
Han, L.Y.1
Cai, C.Z.2
Lo, S.L.3
Chung, M.C.4
Chen, Y.Z.5
-
16
-
-
0346252360
-
Classification of protein quaternary structure with support vector machine
-
Zhang SW, Pan Q, Zhang HC, Zhang YL, Wang HY. Classification of protein quaternary structure with support vector machine. Bioinformatics 2003;19(18):2390-2396.
-
(2003)
Bioinformatics
, vol.19
, Issue.18
, pp. 2390-2396
-
-
Zhang, S.W.1
Pan, Q.2
Zhang, H.C.3
Zhang, Y.L.4
Wang, H.Y.5
-
17
-
-
1442349113
-
Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information
-
Kaur H, Raghava GP. Prediction of alpha-turns in proteins using PSI-BLAST profiles and secondary structure information. Proteins 2004;55(1):83-90.
-
(2004)
Proteins
, vol.55
, Issue.1
, pp. 83-90
-
-
Kaur, H.1
Raghava, G.P.2
-
18
-
-
0036166451
-
Classifying G-protein coupled receptors with support vector machines
-
Karchin R, Karplus K, Haussler D. Classifying G-protein coupled receptors with support vector machines. Bioinformatics 2002;18(1):147-159.
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. 147-159
-
-
Karchin, R.1
Karplus, K.2
Haussler, D.3
-
19
-
-
4043098299
-
Accurate classification of homodimeric vs other homooligomeric proteins using a new measure of information discrepancy
-
Song J, Tang H. Accurate classification of homodimeric vs other homooligomeric proteins using a new measure of information discrepancy. J Chem Inf Comput Sci 2004;44(4):1324-1327.
-
(2004)
J Chem Inf Comput Sci
, vol.44
, Issue.4
, pp. 1324-1327
-
-
Song, J.1
Tang, H.2
-
20
-
-
1442275650
-
Enzyme family classification by support vector machines
-
Cai CZ, Han LY, Ji ZL, Chen YZ. Enzyme family classification by support vector machines. Proteins 2004;55(1):66-76.
-
(2004)
Proteins
, vol.55
, Issue.1
, pp. 66-76
-
-
Cai, C.Z.1
Han, L.Y.2
Ji, Z.L.3
Chen, Y.Z.4
-
21
-
-
0031618972
-
The use of amino acid sequence alignments to assess potential allergenicity of proteins used in genetically modified foods
-
Gendel SM. The use of amino acid sequence alignments to assess potential allergenicity of proteins used in genetically modified foods. Adv Food Nutr Res 1998;42:45-62.
-
(1998)
Adv Food Nutr Res
, vol.42
, pp. 45-62
-
-
Gendel, S.M.1
-
22
-
-
0036260304
-
Sequence analysis for assessing potential allergenicity
-
Gendel SM. Sequence analysis for assessing potential allergenicity. Ann NY Acad Sci 2002;964:87-98.
-
(2002)
Ann NY Acad Sci
, vol.964
, pp. 87-98
-
-
Gendel, S.M.1
-
23
-
-
0036673480
-
Bioinformatic methods for allergenicity assessment using a comprehensive allergen database
-
Hileman RE, Silvanovich A, Goodman RE, et al. Bioinformatic methods for allergenicity assessment using a comprehensive allergen database. Int Arch Allergy Immunol 2002;128(4):280-291.
-
(2002)
Int Arch Allergy Immunol
, vol.128
, Issue.4
, pp. 280-291
-
-
Hileman, R.E.1
Silvanovich, A.2
Goodman, R.E.3
-
24
-
-
25444518424
-
Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE-binding linear epitopes of allergens
-
Kleter GA, Peijnenburg AA. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE-binding linear epitopes of allergens. BMC Struct Biol 2002;2(1):8.
-
(2002)
BMC Struct Biol
, vol.2
, Issue.1
, pp. 8
-
-
Kleter, G.A.1
Peijnenburg, A.A.2
-
25
-
-
0036941115
-
Prediction of food protein allergenicity: A bioinformatic learning systems approach
-
Zorzet A, Gustafsson M, Hammerling U. Prediction of food protein allergenicity: a bioinformatic learning systems approach. In Silico Biol 2002;2:525-534.
-
(2002)
In Silico Biol
, vol.2
, pp. 525-534
-
-
Zorzet, A.1
Gustafsson, M.2
Hammerling, U.3
-
26
-
-
0036772523
-
Data mining of sequences and 3D structures of allergenic proteins
-
Ivanciuc O, Schein CH, Braun W. Data mining of sequences and 3D structures of allergenic proteins. Bioinformatics 2002;18(10):1358-1364.
-
(2002)
Bioinformatics
, vol.18
, Issue.10
, pp. 1358-1364
-
-
Ivanciuc, O.1
Schein, C.H.2
Braun, W.3
-
27
-
-
0037251966
-
SDAP: Database and computational tools for allergenic proteins
-
Ivanciuc O, Schein CH, Braun W. SDAP: database and computational tools for allergenic proteins. Nucleic Acids Res 2003;31(1):359-362.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 359-362
-
-
Ivanciuc, O.1
Schein, C.H.2
Braun, W.3
-
28
-
-
0038380463
-
Allergenicity prediction by protein sequence
-
Stadler MB, Stadler BM. Allergenicity prediction by protein sequence. FASEB J 2003;17(9):1141-1143.
-
(2003)
FASEB J
, vol.17
, Issue.9
, pp. 1141-1143
-
-
Stadler, M.B.1
Stadler, B.M.2
-
29
-
-
1542316862
-
Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms
-
Soeria-Atmadja D, Zorzet A, Gustafsson MG, Hammerling U. Statistical evaluation of local alignment features predicting allergenicity using supervised classification algorithms. Int Arch Allergy Immunol 2004;133(2):101-112.
-
(2004)
Int Arch Allergy Immunol
, vol.133
, Issue.2
, pp. 101-112
-
-
Soeria-Atmadja, D.1
Zorzet, A.2
Gustafsson, M.G.3
Hammerling, U.4
-
30
-
-
8844259689
-
Predicting allergenic proteins using wavelet transform
-
Li KB, Issac P, Krishnan A. Predicting allergenic proteins using wavelet transform. Bioinformatics 2004;20(16):2572-2578.
-
(2004)
Bioinformatics
, vol.20
, Issue.16
, pp. 2572-2578
-
-
Li, K.B.1
Issac, P.2
Krishnan, A.3
-
31
-
-
12744279638
-
Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins
-
Bjorklund AK, Soeria-Atmadja D, Zorzet A, Hammerling U, Gustafsson MG. Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins. Bioinformatics 2005;21(1):39-50.
-
(2005)
Bioinformatics
, vol.21
, Issue.1
, pp. 39-50
-
-
Bjorklund, A.K.1
Soeria-Atmadja, D.2
Zorzet, A.3
Hammerling, U.4
Gustafsson, M.G.5
-
32
-
-
0042622243
-
SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence
-
Cai CZ, Han LY, Ji ZL, Chen X, Chen YZ. SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 2003;31(13):3692-3697.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3692-3697
-
-
Cai, C.Z.1
Han, L.Y.2
Ji, Z.L.3
Chen, X.4
Chen, Y.Z.5
-
33
-
-
0344740820
-
Functional classification of proteins using a nearest neighbour algorithm
-
Keck HP, Wetter T. Functional classification of proteins using a nearest neighbour algorithm. In Silico Biol 2003;3(3):265-275.
-
(2003)
In Silico Biol
, vol.3
, Issue.3
, pp. 265-275
-
-
Keck, H.P.1
Wetter, T.2
-
34
-
-
0027092799
-
Protein classification artificial neural system
-
Wu C, Whitson G, McLarty J, Ermongkonchai A, Chang TC. Protein classification artificial neural system. Protein Sci 1992;1(5):667-677.
-
(1992)
Protein Sci
, vol.1
, Issue.5
, pp. 667-677
-
-
Wu, C.1
Whitson, G.2
McLarty, J.3
Ermongkonchai, A.4
Chang, T.C.5
-
36
-
-
0037076322
-
Selection bias in gene extraction on the basis of microarray gene-expression data
-
Ambroise C, McLachlan GJ. Selection bias in gene extraction on the basis of microarray gene-expression data. Proc Natl Acad Sci USA 2002;99(10):6562- 6566.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.10
, pp. 6562-6566
-
-
Ambroise, C.1
McLachlan, G.J.2
-
37
-
-
1342288007
-
SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence
-
Bhasin M, Raghava GP. SVM based method for predicting HLA-DRB1*0401 binding peptides in an antigen sequence. Bioinformatics 2004;20(3):421-423.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 421-423
-
-
Bhasin, M.1
Raghava, G.P.2
-
38
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz AR, Pisabarro MT, Gago F, Wade RC. Prediction of drug binding affinities by comparative binding energy analysis. J Med Chem 1995;38(14):2681-2691.
-
(1995)
J Med Chem
, vol.38
, Issue.14
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
39
-
-
25444521952
-
Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling
-
Freyhult E, Prusis P, Lapinsh M, Wikberg JE, Moulton V, Gustafsson MG. Unbiased descriptor and parameter selection confirms the potential of proteochemometric modelling. BMC Bioinformatics 2005;6(1):50.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.1
, pp. 50
-
-
Freyhult, E.1
Prusis, P.2
Lapinsh, M.3
Wikberg, J.E.4
Moulton, V.5
Gustafsson, M.G.6
-
40
-
-
0026953919
-
Receiver operating characteristic curves: A basic understanding
-
Vining DJ, Gladish GW. Receiver operating characteristic curves: a basic understanding. Radiographics 1992;12(6):1147-1154.
-
(1992)
Radiographics
, vol.12
, Issue.6
, pp. 1147-1154
-
-
Vining, D.J.1
Gladish, G.W.2
-
41
-
-
0033990061
-
Flexible sequence similarity searching with the FASTA3 program package
-
Pearson WR. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol Biol 2000;132:185-219.
-
(2000)
Methods Mol Biol
, vol.132
, pp. 185-219
-
-
Pearson, W.R.1
-
42
-
-
0003663755
-
-
Faculty EWI-ICT, Delft University of Technology
-
Duin RPW, Juszczak P, Paclik P, Pekalska E, de Ridder D, Tax DMJ. PRTools4, A Matlab Toolbox for Pattern Recognition Research. Faculty EWI-ICT, Delft University of Technology; 2004.
-
(2004)
PRTools4, a Matlab Toolbox for Pattern Recognition Research
-
-
Duin, R.P.W.1
Juszczak, P.2
Paclik, P.3
Pekalska, E.4
De Ridder, D.5
Tax, D.M.J.6
-
43
-
-
3042810008
-
Sequence-based prediction of protein domains
-
Liu J, Rost B. Sequence-based prediction of protein domains. Nucleic Acids Res 2004;32(12):3522-3530.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.12
, pp. 3522-3530
-
-
Liu, J.1
Rost, B.2
-
44
-
-
0027169638
-
Improved prediction of protein secondary structure by use of sequence profiles and neural networks
-
Rost B, Sander C. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc Natl Acad Sci USA 1993;90(16):7558-7562.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, Issue.16
, pp. 7558-7562
-
-
Rost, B.1
Sander, C.2
-
45
-
-
12244271454
-
Predicting CNS permeability of drug molecules: Comparison of neural network and support vector machine algorithms
-
Doniger S, Hofmann T, Yeh J. Predicting CNS permeability of drug molecules: comparison of neural network and support vector machine algorithms. J Comput Biol 2002;9(6):849-864.
-
(2002)
J Comput Biol
, vol.9
, Issue.6
, pp. 849-864
-
-
Doniger, S.1
Hofmann, T.2
Yeh, J.3
|