-
1
-
-
0037020329
-
Drug design strategies for targeting Gprotein-coupled receptors
-
Klabunde, T.; Hessler, G. Drug design strategies for targeting Gprotein-coupled receptors. Chembiochem, 2002, 3(10), 928-944.
-
(2002)
Chembiochem
, vol.3
, Issue.10
, pp. 928-944
-
-
Klabunde, T.1
Hessler, G.2
-
2
-
-
33845275819
-
Estimation of membrane proteins in the human proteome
-
Ahram, M.; Litou, Z.I.; Fang, R.; Al-Tawallbeh, G. Estimation of membrane proteins in the human proteome. In Silico Biol., 2006, 6(5), 379-386.
-
(2006)
In Silico Biol
, vol.6
, Issue.5
, pp. 379-386
-
-
Ahram, M.1
Litou, Z.I.2
Fang, R.3
Al-Tawallbeh, G.4
-
3
-
-
0032570779
-
Do transmembrane protein superfolds exist?
-
Jones, D.T. Do transmembrane protein superfolds exist? FEBS Lett., 1998, 423(3), 281-285.
-
(1998)
FEBS Lett
, vol.423
, Issue.3
, pp. 281-285
-
-
Jones, D.T.1
-
4
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol., 2001, 305(3), 567-580.
-
(2001)
J. Mol. Biol
, vol.305
, Issue.3
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.4
-
5
-
-
0033552649
-
Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system
-
Mitaku, S.; Ono, M.; Hirokawa, T.; Boon-Chieng, S.; Sonoyama, M. Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system. Biophys. Chem., 1999, 82(2-3), 165-171.
-
(1999)
Biophys. Chem.
, vol.82
, Issue.2-3
, pp. 165-171
-
-
Mitaku, S.1
Ono, M.2
Hirokawa, T.3
Boon-Chieng, S.4
Sonoyama, M.5
-
6
-
-
10244252813
-
Transmembrane proteins in the Protein Data Bank: Identification and classification
-
Tusnády, G.; Dosztányi, Z.; Simon, I. Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics, 2004, 20(17), 2964-2972.
-
(2004)
Bioinformatics
, vol.20
, Issue.17
, pp. 2964-2972
-
-
Tusnády, G.1
Dosztányi, Z.2
Simon, I.3
-
7
-
-
13444280419
-
PDB_TM: Selection and membrane localization of transmembrane proteins in the protein data bank
-
Tusnády, G.; Dosztányi, Z.; Simon, I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res., 2005, 33(Database issue), D275-D278.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.Database issue
-
-
Tusnády, G.1
Dosztányi, Z.2
Simon, I.3
-
8
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res., 2000, 28(1), 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
9
-
-
0030983047
-
Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
-
Wallin, E.; Tsukihara, T.; Yoshikawa, S.; von Heijne, G.; Elofsson, A. Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci., 1997, 6(4), 808-815.
-
(1997)
Protein Sci
, vol.6
, Issue.4
, pp. 808-815
-
-
Wallin, E.1
Tsukihara, T.2
Yoshikawa, S.3
von Heijne, G.4
Elofsson, A.5
-
10
-
-
12344330612
-
A study of the membrane-water interface region of membrane proteins
-
Granseth, E.; von Heijne, G.; Elofsson, A. A study of the membrane-water interface region of membrane proteins. J. Mol. Biol., 2005, 346(1), 377-385.
-
(2005)
J. Mol. Biol
, vol.346
, Issue.1
, pp. 377-385
-
-
Granseth, E.1
von Heijne, G.2
Elofsson, A.3
-
11
-
-
34548178234
-
Antidepressant binding site in a bacterial homologue of neurotransmitter transporters
-
Singh, S.K.; Yamashita, A.; Gouaux, E. Antidepressant binding site in a bacterial homologue of neurotransmitter transporters. Nature, 2007, 448(7156), 952-956.
-
(2007)
Nature
, vol.448
, Issue.7156
, pp. 952-956
-
-
Singh, S.K.1
Yamashita, A.2
Gouaux, E.3
-
12
-
-
33746361201
-
Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: Application to complete genomes
-
Viklund, H.; Granseth, E.; Elofsson, A. Structural classification and prediction of reentrant regions in alpha-helical transmembrane proteins: application to complete genomes. J. Mol. Biol., 2006, 361(3), 591-603.
-
(2006)
J. Mol. Biol
, vol.361
, Issue.3
, pp. 591-603
-
-
Viklund, H.1
Granseth, E.2
Elofsson, A.3
-
13
-
-
0025782832
-
Proline kinks in transmembrane alpha-helices
-
von Heijne, G. Proline kinks in transmembrane alpha-helices. J. Mol. Biol., 1991, 218(3), 499-503.
-
(1991)
J. Mol. Biol
, vol.218
, Issue.3
, pp. 499-503
-
-
von Heijne, G.1
-
14
-
-
0031047328
-
Roles of transmembrane prolines and proline-induced kinks of the lutropin/choriogonadotropin receptor
-
Hong, S.; Ryu, K.S.; Oh, M.S.; Ji, I.; Ji, T.H. Roles of transmembrane prolines and proline-induced kinks of the lutropin/choriogonadotropin receptor. J. Biol. Chem., 1997, 272(7), 4166-4171.
-
(1997)
J. Biol. Chem
, vol.272
, Issue.7
, pp. 4166-4171
-
-
Hong, S.1
Ryu, K.S.2
Oh, M.S.3
Ji, I.4
Ji, T.H.5
-
15
-
-
0035895421
-
Non-alphahelical elements modulate polytopic membrane protein architecture
-
Riek, R.P.; Rigoutsos, I.; Novotny, J.; Graham, R.M. Non-alphahelical elements modulate polytopic membrane protein architecture. J. Mol. Biol., 2001, 306(2), 349-362.
-
(2001)
J. Mol. Biol
, vol.306
, Issue.2
, pp. 349-362
-
-
Riek, R.P.1
Rigoutsos, I.2
Novotny, J.3
Graham, R.M.4
-
16
-
-
0742288411
-
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
-
Yohannan, S.; Faham, S.; Yang, D.; Whitelegge, J.P.; Bowie, J.U. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. USA, 2004, 101(4), 959-963.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.4
, pp. 959-963
-
-
Yohannan, S.1
Faham, S.2
Yang, D.3
Whitelegge, J.P.4
Bowie, J.U.5
-
17
-
-
0027122748
-
Proteins. One thousand families for the molecular biologist
-
Chothia, C. Proteins. One thousand families for the molecular biologist. Nature, 1992, 357(6379), 543-544.
-
(1992)
Nature
, vol.357
, Issue.6379
, pp. 543-544
-
-
Chothia, C.1
-
18
-
-
0034674175
-
Estimating the number of protein folds and families from complete genome data
-
Wolf, Y.I.; Grishin, N.V.; Koonin, E.V. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol., 2000, 299(4), 897-905.
-
(2000)
J. Mol. Biol
, vol.299
, Issue.4
, pp. 897-905
-
-
Wolf, Y.I.1
Grishin, N.V.2
Koonin, E.V.3
-
19
-
-
0037079014
-
The structure of the protein universe and genome evolution
-
Koonin, E.V.; Wolf, Y.I.; Karev, G.P. The structure of the protein universe and genome evolution. Nature, 2002, 420(6912), 218-223.
-
(2002)
Nature
, vol.420
, Issue.6912
, pp. 218-223
-
-
Koonin, E.V.1
Wolf, Y.I.2
Karev, G.P.3
-
20
-
-
0033457943
-
Helix-bundle membrane protein fold templates
-
Bowie, J.U. Helix-bundle membrane protein fold templates. Protein Sci., 1999, 8(12), 2711-2719.
-
(1999)
Protein Sci
, vol.8
, Issue.12
, pp. 2711-2719
-
-
Bowie, J.U.1
-
21
-
-
0034057802
-
Membrane topology and insertion of membrane proteins: Search for topogenic signals
-
van Geest, M.; Lolkema, J.S. Membrane topology and insertion of membrane proteins: search for topogenic signals. Microbiol. Mol. Biol. Rev., 2000, 64(1), 13-33.
-
(2000)
Microbiol. Mol. Biol. Rev
, vol.64
, Issue.1
, pp. 13-33
-
-
van Geest, M.1
Lolkema, J.S.2
-
22
-
-
38549172064
-
TOPDB: Topology data bank of transmembrane proteins
-
Tusnády, G.E.; Kalmár, L.; Simon, I. TOPDB: topology data bank of transmembrane proteins. Nucleic Acids Res., 2008, 36(Database issue), D234-D239.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.Database issue
-
-
Tusnády, G.E.1
Kalmár, L.2
Simon, I.3
-
23
-
-
19744376674
-
Global topology analysis of the Escherichia coli inner membrane proteome
-
Daley, D.O.; Rapp, M.; Granseth, E.; Melén, K.; Drew, D.; von Heijne, G. Global topology analysis of the Escherichia coli inner membrane proteome. Science, 2005, 308(5726), 1321-1323.
-
(2005)
Science
, vol.308
, Issue.5726
, pp. 1321-1323
-
-
Daley, D.O.1
Rapp, M.2
Granseth, E.3
Melén, K.4
Drew, D.5
von Heijne, G.6
-
24
-
-
33746616385
-
A global topology map of the Saccharomyces cerevisiae membrane proteome
-
Kim, H.; Melén, K.; Osterberg, M.; von Heijne, G. A global topology map of the Saccharomyces cerevisiae membrane proteome. Proc. Natl. Acad. Sci. USA, 2006, 103(30), 11142-11147.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, Issue.30
, pp. 11142-11147
-
-
Kim, H.1
Melén, K.2
Osterberg, M.3
von Heijne, G.4
-
25
-
-
0000651660
-
The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology
-
von Heijne, G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the transmembrane topology. EMBO J., 1986, 5(11), 3021-3027.
-
(1986)
EMBO J
, vol.5
, Issue.11
, pp. 3021-3027
-
-
von Heijne, G.1
-
26
-
-
0025015646
-
Fine-tuning the topology of a polytopic membrane protein: Role of positively and negatively charged amino acids
-
Nilsson, I.; von Heijne, G. Fine-tuning the topology of a polytopic membrane protein: role of positively and negatively charged amino acids. Cell, 1990, 62(6), 1135-1141.
-
(1990)
Cell
, vol.62
, Issue.6
, pp. 1135-1141
-
-
Nilsson, I.1
von Heijne, G.2
-
27
-
-
0028175016
-
Topological frustration in multispanning E. coli inner membrane proteins
-
Gafvelin, G.; von Heijne, G. Topological frustration in multispanning E. coli inner membrane proteins. Cell, 1994, 77(3), 401-412.
-
(1994)
Cell
, vol.77
, Issue.3
, pp. 401-412
-
-
Gafvelin, G.1
von Heijne, G.2
-
28
-
-
32244436490
-
Identification and evolution of dual-topology membrane proteins
-
Rapp, M.; Granseth, E.; Seppälä, S.; von Heijne, G. Identification and evolution of dual-topology membrane proteins. Nat. Struct. Mol. Biol., 2006, 13(2), 112-116.
-
(2006)
Nat. Struct. Mol. Biol
, vol.13
, Issue.2
, pp. 112-116
-
-
Rapp, M.1
Granseth, E.2
Seppälä, S.3
von Heijne, G.4
-
29
-
-
29344450131
-
X-ray structure of the EmrE multidrug transporter in complex with a substrate
-
Pornillos, O.; Chen, Y.; Chen, A.P.; Chang, G. X-ray structure of the EmrE multidrug transporter in complex with a substrate. Science, 2005, 310(5756), 1950-1953.
-
(2005)
Science
, vol.310
, Issue.5756
, pp. 1950-1953
-
-
Pornillos, O.1
Chen, Y.2
Chen, A.P.3
Chang, G.4
-
30
-
-
34147208836
-
Retraction
-
Chang, G.; Roth, C.B.; Reyes, C.L.; Pornillos, O.; Chen, Y.; Chen, A.P. Retraction. Science, 2006, 314(5807), 1875.
-
(2006)
Science
, vol.314
, Issue.5807
, pp. 1875
-
-
Chang, G.1
Roth, C.B.2
Reyes, C.L.3
Pornillos, O.4
Chen, Y.5
Chen, A.P.6
-
31
-
-
37649009221
-
X-ray structure of EmrE supports dual topology model
-
Chen, Y.; Pornillos, O.; Lieu, S.; Ma, C.; Chen, A.P.; Chang, G. X-ray structure of EmrE supports dual topology model. Proc. Natl. Acad. Sci. USA, 2007, 104(48), 18999-19004.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, Issue.48
, pp. 18999-19004
-
-
Chen, Y.1
Pornillos, O.2
Lieu, S.3
Ma, C.4
Chen, A.P.5
Chang, G.6
-
32
-
-
34249899930
-
When biochemistry meets structural biology: The cautionary tale of EmrE
-
Schuldiner, S. When biochemistry meets structural biology: the cautionary tale of EmrE. Trends Biochem Sci, 2007, 32(6), 252-258.
-
(2007)
Trends Biochem Sci
, vol.32
, Issue.6
, pp. 252-258
-
-
Schuldiner, S.1
-
33
-
-
34547863829
-
Controversy over EmrE structure
-
author reply 748-751
-
Schuldiner, S. Controversy over EmrE structure. Science, 2007, 317(5839), 748-51 author reply 748-751.
-
(2007)
Science
, vol.317
, Issue.5839
, pp. 748-751
-
-
Schuldiner, S.1
-
34
-
-
38049069768
-
Parallel topology of genetically fused EmrE homodimers
-
Steiner-Mordoch, S.; Soskine, M.; Solomon, D.; Rotem, D.; Gold, A.; Yechieli, M.; Adam, Y.; Schuldiner, S. Parallel topology of genetically fused EmrE homodimers. EMBO J., 2008, 27(1), 17-26.
-
(2008)
EMBO J
, vol.27
, Issue.1
, pp. 17-26
-
-
Steiner-Mordoch, S.1
Soskine, M.2
Solomon, D.3
Rotem, D.4
Gold, A.5
Yechieli, M.6
Adam, Y.7
Schuldiner, S.8
-
35
-
-
0034604451
-
Crystal structure of rhodopsin: A G protein-coupled receptor
-
Palczewski, K.; Kumasaka, T.; Hori, T.; Behnke, C.A.; Motoshima, H.; Fox, B.A.; Le Trong, I.; Teller, D.C.; Okada, T.; Stenkamp, R.E.; Yamamoto, M.; Miyano, M. Crystal structure of rhodopsin: A G protein-coupled receptor. Science, 2000, 289(5480), 739-745.
-
(2000)
Science
, vol.289
, Issue.5480
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.A.6
Le Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
Yamamoto, M.11
Miyano, M.12
-
36
-
-
0036893269
-
Transmembrane helix predictions revisited
-
Chen, C.P.; Kernytsky, A.; Rost, B. Transmembrane helix predictions revisited. Protein Sci., 2002, 11(12), 2774-2791.
-
(2002)
Protein Sci
, vol.11
, Issue.12
, pp. 2774-2791
-
-
Chen, C.P.1
Kernytsky, A.2
Rost, B.3
-
37
-
-
34249683488
-
Membrane protein structure: Prediction versus reality
-
Elofsson, A.; von Heijne, G. Membrane protein structure: prediction versus reality. Annu. Rev. Biochem., 2007, 76, 125-140.
-
(2007)
Annu. Rev. Biochem
, vol.76
, pp. 125-140
-
-
Elofsson, A.1
von Heijne, G.2
-
38
-
-
33947213875
-
Membrane protein prediction methods
-
Punta, M.; Forrest, L. R.; Bigelow, H.; Kernytsky, A.; Liu, J.; Rost, B. Membrane protein prediction methods. Methods, 2007, 41(4), 460-474.
-
(2007)
Methods
, vol.41
, Issue.4
, pp. 460-474
-
-
Punta, M.1
Forrest, L.R.2
Bigelow, H.3
Kernytsky, A.4
Liu, J.5
Rost, B.6
-
39
-
-
0001911218
-
State-of-the-art in membrane protein prediction
-
Chen, C.P.; Rost, B. State-of-the-art in membrane protein prediction. Appl. Bioinformatics, 2002, 1(1), 21-35.
-
(2002)
Appl. Bioinformatics
, vol.1
, Issue.1
, pp. 21-35
-
-
Chen, C.P.1
Rost, B.2
-
40
-
-
0042622254
-
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria
-
Gardy, J.L.; Spencer, C.; Wang, K.; Ester, M.; Tusnády, G.E.; Simon, I.; Hua, S.; deFays, K.; Lambert, C.; Nakai, K.; Brinkman, F.S.L. PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res., 2003, 31(13), 3613-3617.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3613-3617
-
-
Gardy, J.L.1
Spencer, C.2
Wang, K.3
Ester, M.4
Tusnády, G.E.5
Simon, I.6
Hua, S.7
Defays, K.8
Lambert, C.9
Nakai, K.10
Brinkman, F.S.L.11
-
41
-
-
0030759333
-
Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method
-
Cserz, 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
-
-
Cserz, M.1
Wallin, E.2
Simon, I.3
von Heijne, G.4
Elofsson, A.5
-
42
-
-
0036763207
-
On filtering false positive transmembrane protein predictions
-
Cserz, M.; Eisenhaber, F.; Eisenhaber, B.; Simon, I. On filtering false positive transmembrane protein predictions. Protein Eng., 2002, 15(9), 745-752.
-
(2002)
Protein Eng
, vol.15
, Issue.9
, pp. 745-752
-
-
Cserz, M.1
Eisenhaber, F.2
Eisenhaber, B.3
Simon, I.4
-
43
-
-
0347093547
-
TM or not TM: Transmembrane protein prediction with low false positive rate using DAS-TMfilter
-
Cserz, M.; Eisenhaber, F.; Eisenhaber, B.; Simon, I. TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics, 2004, 20(1), 136-137.
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 136-137
-
-
Cserz, M.1
Eisenhaber, F.2
Eisenhaber, B.3
Simon, I.4
-
44
-
-
0032561132
-
Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
-
Tusnády, G.E.; Simon, I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol., 1998, 283(2), 489-506.
-
(1998)
J. Mol. Biol
, vol.283
, Issue.2
, pp. 489-506
-
-
Tusnády, G.E.1
Simon, I.2
-
45
-
-
3042579686
-
Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information
-
Viklund, H.; Elofsson, A. Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci., 2004, 13(7), 1908-1917.
-
(2004)
Protein Sci
, vol.13
, Issue.7
, pp. 1908-1917
-
-
Viklund, H.1
Elofsson, A.2
-
46
-
-
18744403991
-
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
-
Kahsay, R.Y.; Gao, G.; Liao, L. An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. Bioinformatics, 2005, 21(9), 1853-1858.
-
(2005)
Bioinformatics
, vol.21
, Issue.9
, pp. 1853-1858
-
-
Kahsay, R.Y.1
Gao, G.2
Liao, L.3
-
47
-
-
2142657817
-
A combined transmembrane topology and signal peptide prediction method
-
Käll, L.; Krogh, A.; Sonnhammer, E.L.L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 2004, 338(5), 1027-1036.
-
(2004)
J. Mol. Biol
, vol.338
, Issue.5
, pp. 1027-1036
-
-
Käll, L.1
Krogh, A.2
Sonnhammer, E.L.L.3
-
48
-
-
29144483361
-
An HMM posterior decoder for sequence feature prediction that includes homology information
-
Käll, L.; Krogh, A.; Sonnhammer, E.L.L. An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics, 2005, 21(Suppl 1), i251-i257.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Käll, L.1
Krogh, A.2
Sonnhammer, E.L.L.3
-
49
-
-
34547584314
-
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server
-
Käll, L.; Krogh, A.; Sonnhammer, E.L.L. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res., 2007, 35(Web Server issue), W429-W432.
-
(2007)
Nucleic Acids Res
, vol.35
, Issue.Web Server issue
-
-
Käll, L.1
Krogh, A.2
Sonnhammer, E.L.L.3
-
50
-
-
57149112523
-
Transmembrane topology and signal peptide prediction using dynamic bayesian networks
-
Reynolds, S.M.; Käll, L.; Riffle, M.E.; Bilmes, J.A.; Noble, W.S. Transmembrane topology and signal peptide prediction using dynamic bayesian networks. PLoS Comput. Biol., 2008, 4(11), e1000213.
-
(2008)
PLoS Comput. Biol
, vol.4
, Issue.11
-
-
Reynolds, S.M.1
Käll, L.2
Riffle, M.E.3
Bilmes, J.A.4
Noble, W.S.5
-
51
-
-
34250883824
-
Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function
-
Lo, A.; Chiu, H.; Sung, T.; Hsu, W. Transmembrane helix and topology prediction using hierarchical SVM classifiers and an alternating geometric scoring function. Comput. Syst. Bioinformatics Conf., 2006, 31-42.
-
(2006)
Comput. Syst. Bioinformatics Conf
, pp. 31-42
-
-
Lo, A.1
Chiu, H.2
Sung, T.3
Hsu, W.4
-
52
-
-
39749179168
-
Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function
-
Lo, A.; Chiu, H.; Sung, T.; Lyu, P.; Hsu, W. Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function. J. Proteome Res., 2008, 7(2), 487-496.
-
(2008)
J. Proteome Res
, vol.7
, Issue.2
, pp. 487-496
-
-
Lo, A.1
Chiu, H.2
Sung, T.3
Lyu, P.4
Hsu, W.5
-
53
-
-
35748979116
-
TMpro web server and web service: Transmembrane helix prediction through amino acid property analysis
-
Ganapathiraju, M.; Jursa, C.J.; Karimi, H.A.; Klein-Seetharaman, J. TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. Bioinformatics, 2007, 23(20), 2795-2796.
-
(2007)
Bioinformatics
, vol.23
, Issue.20
, pp. 2795-2796
-
-
Ganapathiraju, M.1
Jursa, C.J.2
Karimi, H.A.3
Klein-Seetharaman, J.4
-
54
-
-
84872004750
-
Transmembrane helix prediction using amino acid property features and latent semantic analysis
-
Ganapathiraju, M.; Balakrishnan, N.; Reddy, R.; Klein-Seetharaman, J. Transmembrane helix prediction using amino acid property features and latent semantic analysis. BMC Bioinformatics, 2008, 9(Suppl 1), S4.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 1
-
-
Ganapathiraju, M.1
Balakrishnan, N.2
Reddy, R.3
Klein-Seetharaman, J.4
-
55
-
-
0035836704
-
Prion protein: Evolution caught en route
-
Tompa, P.; Tusnády, G.E.; Cserzo, M.; Simon, I. Prion protein: evolution caught en route. Proc. Natl. Acad. Sci. USA, 2001, 98(8), 4431-4436.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, Issue.8
, pp. 4431-4436
-
-
Tompa, P.1
Tusnády, G.E.2
Cserzo, M.3
Simon, I.4
-
56
-
-
26444578263
-
SOSUIsignal: Software system for prediction of signal peptide and membrane protein
-
Gomi, M.; Akazawa, F.; Mitaku, S. SOSUIsignal: software system for prediction of signal peptide and membrane protein. Genome Informatics, 2000, 11, 414-415.
-
(2000)
Genome Informatics
, vol.11
, pp. 414-415
-
-
Gomi, M.1
Akazawa, F.2
Mitaku, S.3
-
57
-
-
0344064078
-
Computational differentiation of N-terminal signal peptides and transmembrane helices
-
Yuan, Z.; Davis, M.J.; Zhang, F.; Teasdale, R.D. Computational differentiation of N-terminal signal peptides and transmembrane helices. Biochem. Biophys. Res. Commun., 2003, 312(4), 1278-1283.
-
(2003)
Biochem. Biophys. Res. Commun
, vol.312
, Issue.4
, pp. 1278-1283
-
-
Yuan, Z.1
Davis, M.J.2
Zhang, F.3
Teasdale, R.D.4
-
58
-
-
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
-
59
-
-
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
-
60
-
-
3042521098
-
Improved prediction of signal peptides: SignalP 3.0
-
Bendtsen, J.D.; 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
-
61
-
-
57249083976
-
SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology
-
Viklund, H.; Bernsel, A.; Skwark, M.; Elofsson, A. SPOCTOPUS: A combined predictor of signal peptides and membrane protein topology. Bioinformatics, 2008, 24(24), 2928-2929.
-
(2008)
Bioinformatics
, vol.24
, Issue.24
, pp. 2928-2929
-
-
Viklund, H.1
Bernsel, A.2
Skwark, M.3
Elofsson, A.4
-
62
-
-
0036936886
-
Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction
-
Lao, D.M.; Okuno, T.; Shimizu, T. Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. In Silico Biol., 2002, 2(4), 485-494.
-
(2002)
In Silico Biol
, vol.2
, Issue.4
, pp. 485-494
-
-
Lao, D.M.1
Okuno, T.2
Shimizu, T.3
-
63
-
-
0036947980
-
The presence of signal peptide significantly affects transmembrane topology prediction
-
Lao, D.M.; Arai, M.; Ikeda, M.; Shimizu, T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics, 2002, 18(12), 1562-1566.
-
(2002)
Bioinformatics
, vol.18
, Issue.12
, pp. 1562-1566
-
-
Lao, D.M.1
Arai, M.2
Ikeda, M.3
Shimizu, T.4
-
64
-
-
0023645034
-
Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins
-
Cornette, J.L.; Cease, K.B.; Margalit, H.; Spouge, J.L.; Berzofsky, J.A.; DeLisi, C. Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. J. Mol. Biol., 1987, 195(3), 659-685.
-
(1987)
J. Mol. Biol
, vol.195
, Issue.3
, pp. 659-685
-
-
Cornette, J.L.1
Cease, K.B.2
Margalit, H.3
Spouge, J.L.4
Berzofsky, J.A.5
Delisi, C.6
-
65
-
-
0036248952
-
The prediction of amphiphilic alpha-helices
-
Phoenix, D.A.; Harris, F.; Daman, O.A.; Wallace, J. The prediction of amphiphilic alpha-helices. Curr. Protein Pept. Sci., 2002, 3(2), 201-221.
-
(2002)
Curr. Protein Pept. Sci
, vol.3
, Issue.2
, pp. 201-221
-
-
Phoenix, D.A.1
Harris, F.2
Daman, O.A.3
Wallace, J.4
-
66
-
-
34247595392
-
Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins
-
Wolfenden, R. Experimental measures of amino acid hydrophobicity and the topology of transmembrane and globular proteins. J. Gen. Physiol., 2007, 129(5), 357-362.
-
(2007)
J. Gen. Physiol
, vol.129
, Issue.5
, pp. 357-362
-
-
Wolfenden, R.1
-
67
-
-
0028104942
-
New alignment strategy for transmembrane proteins
-
Cserz, M.; Bernassau, J.M.; Simon, I.; Maigret, B. New alignment strategy for transmembrane proteins. J. Mol. Biol., 1994, 243(3), 388-396.
-
(1994)
J. Mol. Biol
, vol.243
, Issue.3
, pp. 388-396
-
-
Cserz, M.1
Bernassau, J.M.2
Simon, I.3
Maigret, B.4
-
68
-
-
48349146731
-
Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics
-
Kitsas, I.K.; Hadjileontiadis, L.J.; Panas, S.M. Transmembrane helix prediction in proteins using hydrophobicity properties and higher-order statistics. Comput. Biol. Med., 2008, 38(8), 867-880.
-
(2008)
Comput. Biol. Med
, vol.38
, Issue.8
, pp. 867-880
-
-
Kitsas, I.K.1
Hadjileontiadis, L.J.2
Panas, S.M.3
-
69
-
-
48749084114
-
MemBrain: Improving the accuracy of predicting transmembrane helices
-
Shen, H.; Chou, J.J. MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One, 2008, 3(6), e2399.
-
(2008)
PLoS One
, vol.3
, Issue.6
-
-
Shen, H.1
Chou, J.J.2
-
70
-
-
44449083478
-
Prediction of membrane-protein topology from first principles
-
Bernsel, A.; Viklund, H.; Falk, J.; Lindahl, E.; von Heijne, G.; Elofsson, A. Prediction of membrane-protein topology from first principles. Proc. Natl. Acad. Sci. USA, 2008, 105(20), 7177-7181.
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, Issue.20
, pp. 7177-7181
-
-
Bernsel, A.1
Viklund, H.2
Falk, J.3
Lindahl, E.4
von Heijne, G.5
Elofsson, A.6
-
71
-
-
2542452829
-
Cotranslational membrane protein biogenesis at the endoplasmic reticulum
-
Alder, N.N.; Johnson, A.E. Cotranslational membrane protein biogenesis at the endoplasmic reticulum. J. Biol. Chem., 2004, 279(22), 22787-22790.
-
(2004)
J. Biol. Chem
, vol.279
, Issue.22
, pp. 22787-22790
-
-
Alder, N.N.1
Johnson, A.E.2
-
72
-
-
4644356464
-
Membrane-protein integration and the role of the translocation channel
-
Rapoport, T.A.; Goder, V.; Heinrich, S.U.; Matlack, K.E.S. Membrane-protein integration and the role of the translocation channel. Trends Cell Biol., 2004, 14(10), 568-575.
-
(2004)
Trends Cell Biol
, vol.14
, Issue.10
, pp. 568-575
-
-
Rapoport, T.A.1
Goder, V.2
Heinrich, S.U.3
Matlack, K.E.S.4
-
73
-
-
13444262028
-
Recognition of transmembrane helices by the endoplasmic reticulum translocon
-
Hessa, T.; Kim, H.; Bihlmaier, K.; Lundin, C.; Boekel, J.; Ersson, H.; Nilsson, I.; White, S.H.; von Heijne, G. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature, 2005, 433(7024), 377-381.
-
(2005)
Nature
, vol.433
, Issue.7024
, pp. 377-381
-
-
Hessa, T.1
Kim, H.2
Bihlmaier, K.3
Lundin, C.4
Boekel, J.5
Ersson, H.6
Nilsson, I.7
White, S.H.8
von Heijne, G.9
-
74
-
-
37249037182
-
Molecular code for transmembrane-helix recognition by the Sec61 translocon
-
Hessa, T.; Meindl-Beinker, N.M.; Bernsel, A.; Kim, H.; Sato, Y.; Lerch-Bader, M.; Nilsson, I.; White, S.H.; von Heijne, G. Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature, 2007, 450(7172), 1026-1030.
-
(2007)
Nature
, vol.450
, Issue.7172
, pp. 1026-1030
-
-
Hessa, T.1
Meindl-Beinker, N.M.2
Bernsel, A.3
Kim, H.4
Sato, Y.5
Lerch-Bader, M.6
Nilsson, I.7
White, S.H.8
von Heijne, G.9
-
75
-
-
24644490119
-
Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes
-
Nilsson, J.; Persson, B.; von Heijne, G. Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes. Proteins, 2005, 60(4), 606-616.
-
(2005)
Proteins
, vol.60
, Issue.4
, pp. 606-616
-
-
Nilsson, J.1
Persson, B.2
von Heijne, G.3
-
76
-
-
0026716643
-
Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
-
von Heijne, G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 1992, 225(2), 487-494.
-
(1992)
J. Mol. Biol
, vol.225
, Issue.2
, pp. 487-494
-
-
von Heijne, G.1
-
77
-
-
0028211273
-
A model recognition approach to the prediction of all-helical membrane protein structure and topology
-
Jones, D.T.; Taylor, W.R.; Thornton, J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry, 1994, 33(10), 3038-3049.
-
(1994)
Biochemistry
, vol.33
, Issue.10
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
78
-
-
0031614678
-
A hidden Markov model for predicting transmembrane helices in protein sequences
-
Sonnhammer, E.L.; von Heijne, G.; Krogh, A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 1998, 6, 175-182.
-
(1998)
Proc. Int. Conf. Intell. Syst. Mol. Biol
, vol.6
, pp. 175-182
-
-
Sonnhammer, E.L.1
von Heijne, G.2
Krogh, A.3
-
79
-
-
4944242989
-
An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins
-
Martelli, P.L.; Fariselli, P.; Casadio, R. An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins. Bioinformatics, 2003, 19(Suppl 1), i205-i211.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL. 1
-
-
Martelli, P.L.1
Fariselli, P.2
Casadio, R.3
-
80
-
-
0037633968
-
Predicting the topology of transmembrane helical proteins using mean burial propensity and a hiddenMarkov-model-based method
-
Zhou, H.; Zhou, Y. Predicting the topology of transmembrane helical proteins using mean burial propensity and a hiddenMarkov-model-based method. Protein Sci., 2003, 12(7), 1547-1555.
-
(2003)
Protein Sci
, vol.12
, Issue.7
, pp. 1547-1555
-
-
Zhou, H.1
Zhou, Y.2
-
81
-
-
9544252210
-
A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction
-
Zheng, W.J.; Spassov, V.Z.; Yan, L.; Flook, P.K.; Szalma, S. A hidden Markov model with molecular mechanics energy-scoring function for transmembrane helix prediction. Comput. Biol. Chem., 2004, 28(4), 265-274.
-
(2004)
Comput. Biol. Chem
, vol.28
, Issue.4
, pp. 265-274
-
-
Zheng, W.J.1
Spassov, V.Z.2
Yan, L.3
Flook, P.K.4
Szalma, S.5
-
82
-
-
33947417295
-
A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins
-
Fariselli, P.; Martelli, P.L.; Casadio, R. A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins. BMC Bioinformatics, 2005, 6(Suppl.) 4, S12.
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.4
-
-
Fariselli, P.1
Martelli, P.L.2
Casadio, R.3
-
83
-
-
48249151108
-
OCTOPUS: Improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
-
Viklund, H.; Elofsson, A. OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics, 2008, 24(15), 1662-1668.
-
(2008)
Bioinformatics
, vol.24
, Issue.15
, pp. 1662-1668
-
-
Viklund, H.1
Elofsson, A.2
-
84
-
-
34047151404
-
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
-
Jones, D.T. Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics, 2007, 23(5), 538-544.
-
(2007)
Bioinformatics
, vol.23
, Issue.5
, pp. 538-544
-
-
Jones, D.T.1
-
85
-
-
0024610919
-
A tutorial on hidden Markov models and selected applications in speech recognition
-
Rabiner, L. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 1989, 77(2), 257-286.
-
(1989)
Proc. IEEE
, vol.77
, Issue.2
, pp. 257-286
-
-
Rabiner, L.1
-
86
-
-
0036132818
-
Transmembrane topology prediction methods: A re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies
-
Ikeda, M.; Arai, M.; Lao, D.M.; Shimizu, T. Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol., 2002, 2(1), 19-33.
-
(2002)
In Silico Biol
, vol.2
, Issue.1
, pp. 19-33
-
-
Ikeda, M.1
Arai, M.2
Lao, D.M.3
Shimizu, T.4
-
87
-
-
0034899781
-
Evaluation of methods for the prediction of membrane spanning regions
-
Möller, S.; Croning, M.D.; Apweiler, R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics, 2001, 17(7), 646-653.
-
(2001)
Bioinformatics
, vol.17
, Issue.7
, pp. 646-653
-
-
Möller, S.1
Croning, M.D.2
Apweiler, R.3
-
88
-
-
0041620242
-
BPROMPT: A consensus server for membrane protein prediction
-
Taylor, P.D.; Attwood, T.K.; Flower, D.R. BPROMPT: A consensus server for membrane protein prediction. Nucleic Acids Res., 2003, 31(13), 3698-3700.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3698-3700
-
-
Taylor, P.D.1
Attwood, T.K.2
Flower, D.R.3
-
89
-
-
0842308529
-
ConPred_elite: A highly reliable approach to transmembrane topology predication
-
Xia, J.; Ikeda, M.; Shimizu, T. ConPred_elite: a highly reliable approach to transmembrane topology predication. Comput. Biol. Chem., 2004, 28(1), 51-60.
-
(2004)
Comput. Biol. Chem
, vol.28
, Issue.1
, pp. 51-60
-
-
Xia, J.1
Ikeda, M.2
Shimizu, T.3
-
90
-
-
3242891271
-
ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability
-
Arai, M.; Mitsuke, H.; Ikeda, M.; Xia, J.; Kikuchi, T.; Satake, M.; Shimizu, T. ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res., 2004, 32(Web Server issue), W390-W393.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.Web Server issue
-
-
Arai, M.1
Mitsuke, H.2
Ikeda, M.3
Xia, J.4
Kikuchi, T.5
Satake, M.6
Shimizu, T.7
-
91
-
-
0034672544
-
Consensus predictions of membrane protein topology
-
Nilsson, J.; Persson, B.; von Heijne, G. Consensus predictions of membrane protein topology. FEBS Lett., 2000, 486(3), 267-269.
-
(2000)
FEBS Lett
, vol.486
, Issue.3
, pp. 267-269
-
-
Nilsson, J.1
Persson, B.2
von Heijne, G.3
-
92
-
-
0036891703
-
Prediction of partial membrane protein topologies using a consensus approach
-
Nilsson, J.; Persson, B.; Von Heijne, G. Prediction of partial membrane protein topologies using a consensus approach. Protein Sci., 2002, 11(12), 2974-2980.
-
(2002)
Protein Sci
, vol.11
, Issue.12
, pp. 2974-2980
-
-
Nilsson, J.1
Persson, B.2
von Heijne, G.3
-
93
-
-
0034495418
-
A collection of well characterised integral membrane proteins
-
Möller, S.; Kriventseva, E.V.; Apweiler, R. A collection of well characterised integral membrane proteins. Bioinformatics, 2000, 16(12), 1159-1160.
-
(2000)
Bioinformatics
, vol.16
, Issue.12
, pp. 1159-1160
-
-
Möller, S.1
Kriventseva, E.V.2
Apweiler, R.3
-
94
-
-
0037249645
-
TMPDB: A database of experimentally-characterized transmembrane topologies
-
Ikeda, M.; Arai, M.; Okuno, T.; Shimizu, T. TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res., 2003, 31(1), 406-409.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 406-409
-
-
Ikeda, M.1
Arai, M.2
Okuno, T.3
Shimizu, T.4
-
95
-
-
0042121119
-
Static benchmarking of membrane helix predictions
-
Kernytsky, A.; Rost, B. Static benchmarking of membrane helix predictions. Nucleic Acids Res., 2003, 31(13), 3642-3644.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3642-3644
-
-
Kernytsky, A.1
Rost, B.2
-
96
-
-
0034888209
-
A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: The OrienTM algorithm
-
Liakopoulos, T.D.; Pasquier, C.; Hamodrakas, S.J. A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. Protein Eng., 2001, 14(6), 387-390.
-
(2001)
Protein Eng
, vol.14
, Issue.6
, pp. 387-390
-
-
Liakopoulos, T.D.1
Pasquier, C.2
Hamodrakas, S.J.3
-
97
-
-
0344406716
-
Reliability measures for membrane protein topology prediction algorithms
-
Melén, K.; Krogh, A.; von Heijne, G. Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol., 2003, 327(3), 735-744.
-
(2003)
J. Mol. Biol
, vol.327
, Issue.3
, pp. 735-744
-
-
Melén, K.1
Krogh, A.2
von Heijne, G.3
-
98
-
-
27644479960
-
SPdb-a signal peptide database
-
Choo, K.H.; Tan, T.W.; Ranganathan, S. SPdb-a signal peptide database. BMC Bioinformatics, 2005, 6, 249.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 249
-
-
Choo, K.H.1
Tan, T.W.2
Ranganathan, S.3
-
99
-
-
33747879895
-
A combinatorial pattern discovery approach for the prediction of membrane dipping (reentrant) loops
-
Lasso, G.; Antoniw, J.F.; Mullins, J.G.L. A combinatorial pattern discovery approach for the prediction of membrane dipping (reentrant) loops. Bioinformatics, 2006, 22(14), e290-e297.
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Lasso, G.1
Antoniw, J.F.2
Mullins, J.G.L.3
-
100
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann, B.; Bairoch, A.; Apweiler, R.; Blatter, M.; Estreicher, A.; Gasteiger, E.; Martin, M.J.; Michoud, K.; O'Donovan, C.; Phan, I.; Pilbout, S.; Schneider, M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 2003, 31(1), 365-370.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.1
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.4
Estreicher, A.5
Gasteiger, E.6
Martin, M.J.7
Michoud, K.8
O'Donovan, C.9
Phan, I.10
Pilbout, S.11
Schneider, M.12
-
101
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnády, G.E.; Simon, I. The HMMTOP transmembrane topology prediction server. Bioinformatics, 2001, 17(9), 849-850.
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 849-850
-
-
Tusnády, G.E.1
Simon, I.2
-
102
-
-
22244451035
-
Improved membrane protein topology prediction by domain assignments
-
Bernsel, A.; von Heijne, G. Improved membrane protein topology prediction by domain assignments. Protein Sci., 2005, 14(7), 1723-1728.
-
(2005)
Protein Sci
, vol.14
, Issue.7
, pp. 1723-1728
-
-
Bernsel, A.1
von Heijne, G.2
-
103
-
-
33645297088
-
The use of functional domains to improve transmembrane protein topology prediction
-
Xu, E.W.; Kearney, P.; Brown, D.G. The use of functional domains to improve transmembrane protein topology prediction. J. Bioinform. Comput. Biol., 2006, 4(1), 109-123.
-
(2006)
J. Bioinform. Comput. Biol
, vol.4
, Issue.1
, pp. 109-123
-
-
Xu, E.W.1
Kearney, P.2
Brown, D.G.3
-
104
-
-
33847155026
-
Algorithms for incorporating prior topological information in HMMs: Application to transmembrane proteins
-
Bagos, P.G.; Liakopoulos, T.D.; Hamodrakas, S.J. Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics, 2006, 7, 189.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 189
-
-
Bagos, P.G.1
Liakopoulos, T.D.2
Hamodrakas, S.J.3
-
105
-
-
1842611517
-
Experimentally based topology models for E. coli inner membrane proteins
-
Rapp, M.; Drew, D.; Daley, D.O.; Nilsson, J.; Carvalho, T.; Melén, K.; De Gier, J.; Von Heijne, G. Experimentally based topology models for E. coli inner membrane proteins. Protein Sci., 2004, 13(4), 937-945.
-
(2004)
Protein Sci
, vol.13
, Issue.4
, pp. 937-945
-
-
Rapp, M.1
Drew, D.2
Daley, D.O.3
Nilsson, J.4
Carvalho, T.5
Melén, K.6
de Gier, J.7
von Heijne, G.8
-
106
-
-
0038701655
-
Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions
-
Kim, H.; Melén, K.; von Heijne, G. Topology models for 37 Saccharomyces cerevisiae membrane proteins based on C-terminal reporter fusions and predictions. J. Biol. Chem., 2003, 278(12), 10208-10213.
-
(2003)
J. Biol. Chem
, vol.278
, Issue.12
, pp. 10208-10213
-
-
Kim, H.1
Melén, K.2
von Heijne, G.3
-
107
-
-
0037022611
-
Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis
-
Drew, D.; Sjöstrand, D.; Nilsson, J.; Urbig, T.; Chin, C.; de Gier, J.; von Heijne, G. Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis. Proc. Natl. Acad. Sci. USA, 2002, 99(5), 2690-2695.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.5
, pp. 2690-2695
-
-
Drew, D.1
Sjöstrand, D.2
Nilsson, J.3
Urbig, T.4
Chin, C.5
de Gier, J.6
von Heijne, G.7
-
108
-
-
0345864022
-
SMART 4.0: Towards genomic data integration
-
Letunic, I.; Copley, R.R.; Schmidt, S.; Ciccarelli, F.D.; Doerks, T.; Schultz, J.; Ponting, C.P.; Bork, P. SMART 4.0: towards genomic data integration. Nucleic Acids Res., 2004, 32(Database issue), D142-D144.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.Database issue
-
-
Letunic, I.1
Copley, R.R.2
Schmidt, S.3
Ciccarelli, F.D.4
Doerks, T.5
Schultz, J.6
Ponting, C.P.7
Bork, P.8
-
109
-
-
24044436844
-
Experimentally constrained topology models for 51,208 bacterial inner membrane proteins
-
Granseth, E.; Daley, D.O.; Rapp, M.; Melén, K.; von Heijne, G. Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J. Mol. Biol., 2005, 352(3), 489-494.
-
(2005)
J. Mol. Biol
, vol.352
, Issue.3
, pp. 489-494
-
-
Granseth, E.1
Daley, D.O.2
Rapp, M.3
Melén, K.4
von Heijne, G.5
-
110
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn, R.D.; Mistry, J.; Schuster-Böckler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S.R.; Sonnhammer, E.L.L.; Bateman, A. Pfam: clans, web tools and services. Nucleic Acids Res., 2006, 34(Database issue), D247-D251.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.Database issue
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Böckler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.L.12
Bateman, A.13
-
111
-
-
33747843417
-
Localizome: A server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information
-
Lee, S.; Lee, B.; Jang, I.; Kim, S.; Bhak, J. Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res., 2006, 34(Web Server issue), W99-W103.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.Web Server issue
-
-
Lee, S.1
Lee, B.2
Jang, I.3
Kim, S.4
Bhak, J.5
-
112
-
-
45449101527
-
TOPDOM: Database of domains and motifs with conservative location in transmembrane proteins
-
Tusnády, G.E.; Kalmár, L.; Hegyi, H.; Tompa, P.; Simon, I. TOPDOM: database of domains and motifs with conservative location in transmembrane proteins. Bioinformatics, 2008, 24(12), 1469-1470.
-
(2008)
Bioinformatics
, vol.24
, Issue.12
, pp. 1469-1470
-
-
Tusnády, G.E.1
Kalmár, L.2
Hegyi, H.3
Tompa, P.4
Simon, I.5
-
113
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
-
Wallin, E.; von Heijne, G. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci., 1998, 7(4), 1029-1038.
-
(1998)
Protein Sci
, vol.7
, Issue.4
, pp. 1029-1038
-
-
Wallin, E.1
von Heijne, G.2
-
114
-
-
0037132511
-
Reliability of transmembrane predictions in whole-genome data
-
Käll, L.; Sonnhammer, E.L.L. Reliability of transmembrane predictions in whole-genome data. FEBS Lett., 2002, 532(3), 415-418.
-
(2002)
FEBS Lett
, vol.532
, Issue.3
, pp. 415-418
-
-
Käll, L.1
Sonnhammer, E.L.L.2
-
115
-
-
33646366164
-
Towards genomescale structure prediction for transmembrane proteins
-
Hurwitz, N.; Pellegrini-Calace, M.; Jones, D.T. Towards genomescale structure prediction for transmembrane proteins. Philos. Trans. R Soc. Lond. B Biol. Sci., 2006, 361(1467), 465-475.
-
(2006)
Philos. Trans. R Soc. Lond. B Biol. Sci
, vol.361
, Issue.1467
, pp. 465-475
-
-
Hurwitz, N.1
Pellegrini-Calace, M.2
Jones, D.T.3
-
116
-
-
2942567744
-
Global analysis of predicted proteomes: Functional adaptation of physical properties
-
Knight, C.G.; Kassen, R.; Hebestreit, H.; Rainey, P.B. Global analysis of predicted proteomes: functional adaptation of physical properties. Proc. Natl. Acad. Sci. USA, 2004, 101(22), 8390-8395.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.22
, pp. 8390-8395
-
-
Knight, C.G.1
Kassen, R.2
Hebestreit, H.3
Rainey, P.B.4
-
117
-
-
0027509460
-
Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions
-
Boyd, D.; Traxler, B.; Beckwith, J. Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions. J. Bacteriol., 1993, 175(2), 553-556.
-
(1993)
J. Bacteriol
, vol.175
, Issue.2
, pp. 553-556
-
-
Boyd, D.1
Traxler, B.2
Beckwith, J.3
-
118
-
-
0023883641
-
Genetic analysis of the membrane insertion and topology of MalF, a cytoplasmic membrane protein of Escherichia coli
-
Froshauer, S.; Green, G.N.; Boyd, D.; McGovern, K.; Beckwith, J. Genetic analysis of the membrane insertion and topology of MalF, a cytoplasmic membrane protein of Escherichia coli. J. Mol. Biol., 1988, 200(3), 501-511.
-
(1988)
J. Mol. Biol
, vol.200
, Issue.3
, pp. 501-511
-
-
Froshauer, S.1
Green, G.N.2
Boyd, D.3
McGovern, K.4
Beckwith, J.5
-
119
-
-
0025053613
-
Beta-lactamase as a probe of membrane protein assembly and protein export
-
Broome-Smith, J.K.; Tadayyon, M.; Zhang, Y. Beta-lactamase as a probe of membrane protein assembly and protein export. Mol. Microbiol., 1990, 4(10), 1637-1644.
-
(1990)
Mol. Microbiol
, vol.4
, Issue.10
, pp. 1637-1644
-
-
Broome-Smith, J.K.1
Tadayyon, M.2
Zhang, Y.3
-
120
-
-
0035815754
-
Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation
-
Deak, P.M.; Wolf, D.H. Membrane topology and function of Der3/Hrd1p as a ubiquitin-protein ligase (E3) involved in endoplasmic reticulum degradation. J. Biol. Chem., 2001, 276(14), 10663-10669.
-
(2001)
J. Biol. Chem
, vol.276
, Issue.14
, pp. 10663-10669
-
-
Deak, P.M.1
Wolf, D.H.2
-
121
-
-
0028902788
-
Transmembrane helices predicted at 95% accuracy
-
Rost, B.; Casadio, R.; Fariselli, P.; Sander, C. Transmembrane helices predicted at 95% accuracy. Protein Sci., 1995, 4(3), 521-533.
-
(1995)
Protein Sci
, vol.4
, Issue.3
, pp. 521-533
-
-
Rost, B.1
Casadio, R.2
Fariselli, P.3
Sander, C.4
-
122
-
-
0030038634
-
Topology prediction for helical transmembrane proteins at 86% accuracy
-
Rost, B.; Fariselli, P.; Casadio, R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci., 1996, 5(8), 1704-1718.
-
(1996)
Protein Sci
, vol.5
, Issue.8
, pp. 1704-1718
-
-
Rost, B.1
Fariselli, P.2
Casadio, R.3
-
123
-
-
0035109170
-
MPtopo: A database of membrane protein topology
-
Jayasinghe, S.; Hristova, K.; White, S.H. MPtopo: A database of membrane protein topology. Protein Sci., 2001, 10(2), 455-458.
-
(2001)
Protein Sci
, vol.10
, Issue.2
, pp. 455-458
-
-
Jayasinghe, S.1
Hristova, K.2
White, S.H.3
-
124
-
-
3042621274
-
The progress of membrane protein structure determination
-
White, S.H. The progress of membrane protein structure determination. Protein Sci., 2004, 13(7), 1948-1949.
-
(2004)
Protein Sci
, vol.13
, Issue.7
, pp. 1948-1949
-
-
White, S.H.1
-
125
-
-
38649141141
-
Estimating the length of transmembrane helices using Z-coordinate predictions
-
Papaloukas, C.; Granseth, E.; Viklund, H.; Elofsson, A. Estimating the length of transmembrane helices using Z-coordinate predictions. Protein Sci., 2008, 17(2), 271-278.
-
(2008)
Protein Sci
, vol.17
, Issue.2
, pp. 271-278
-
-
Papaloukas, C.1
Granseth, E.2
Viklund, H.3
Elofsson, A.4
-
126
-
-
33644861214
-
OPM: Orientations of proteins in membranes database
-
Lomize, M.A.; Lomize, A.L.; Pogozheva, I.D.; Mosberg, H.I. OPM: orientations of proteins in membranes database. Bioinformatics, 2006, 22(5), 623-625.
-
(2006)
Bioinformatics
, vol.22
, Issue.5
, pp. 623-625
-
-
Lomize, M.A.1
Lomize, A.L.2
Pogozheva, I.D.3
Mosberg, H.I.4
-
127
-
-
33744490360
-
Positioning of proteins in membranes: A computational approach
-
Lomize, A.L.; Pogozheva, I.D.; Lomize, M.A.; Mosberg, H.I. Positioning of proteins in membranes: a computational approach. Protein Sci., 2006, 15(6), 1318-1333.
-
(2006)
Protein Sci
, vol.15
, Issue.6
, pp. 1318-1333
-
-
Lomize, A.L.1
Pogozheva, I.D.2
Lomize, M.A.3
Mosberg, H.I.4
-
128
-
-
33644873454
-
TCDB: The Transporter Classification Database for membrane transport protein analyses and information
-
Saier, M.H.; Tran, C.V.; Barabote, R.D. TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res., 2006, 34(Database issue), D181-D186.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.Database issue
-
-
Saier, M.H.1
Tran, C.V.2
Barabote, R.D.3
|