-
1
-
-
0035424963
-
In vitro display technologies: Novel developments and applications
-
doi:10.1016/S0958-1669(00)00234-2
-
Amstutz, P. et al. 2001 In vitro display technologies: novel developments and applications. Curr. Opin. Biotechnol. 12, 400-405. (doi:10.1016/S0958- 1669(00)00234-2)
-
(2001)
Curr. Opin. Biotechnol.
, vol.12
, pp. 400-405
-
-
Amstutz, P.1
-
2
-
-
0029916911
-
The SWISS-PROT protein sequence data bank and its new supplement TrEMBL
-
doi:10.1093/nar/24.1.21
-
Bairoch, A. & Apweiler, R. 1996 The SWISS-PROT protein sequence data bank and its new supplement TrEMBL. Nucleic Acids Res. 24, 21-25. (doi:10.1093/nar/24.1.21)
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 21-25
-
-
Bairoch, A.1
Apweiler, R.2
-
3
-
-
0033954256
-
The Protein Data Bank
-
doi:10.1093/nar/28.1.235
-
Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. 2000 The Protein Data Bank. Nucleic Acids Res. 28, 235-242. (doi:10.1093/nar/28.1.235)
-
(2000)
Nucleic Acids Res.
, vol.28
, 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
-
4
-
-
0037339560
-
Computer simulations of membrane protein folding: Structure and dynamics
-
Chen, C. M. & Chen, C. C. 2003 Computer simulations of membrane protein folding: structure and dynamics. Biophys. J. 84, 1902-1908.
-
(2003)
Biophys. J.
, vol.84
, pp. 1902-1908
-
-
Chen, C.M.1
Chen, C.C.2
-
5
-
-
0027465713
-
Modeling the transmembrane seven helix bundles
-
Cronet, P., Sander, C. & Vriend, G. 1993 Modeling the transmembrane seven helix bundles. Protein Eng. 6, 59-64.
-
(1993)
Protein Eng.
, vol.6
, pp. 59-64
-
-
Cronet, P.1
Sander, C.2
Vriend, G.3
-
6
-
-
0347093547
-
TM or not TM: Transmembrane protein prediction with low false positive rate using DAS-TMfilter
-
doi:10.1093/bioinformatics/btg394
-
Cserzo, M., Eisenhaber, F., Eisenhaber, B. & Simon, I. 2004 TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics 20, 136-137. (doi:10.1093/bioinformatics/btg394)
-
(2004)
Bioinformatics
, vol.20
, pp. 136-137
-
-
Cserzo, M.1
Eisenhaber, F.2
Eisenhaber, B.3
Simon, I.4
-
7
-
-
0031442678
-
The seven-transmembrane spanning topography of the Alzheimer disease-related presenilin proteins in the plasma membranes of cultured cells
-
doi:10.1073/pnas.94.25.14025
-
Dewji, N. & Singer, S. J. 1997 The seven-transmembrane spanning topography of the Alzheimer disease-related presenilin proteins in the plasma membranes of cultured cells. Proc. Natl Acad. Sci. USA 94, 14025-14030. (doi:10.1073/pnas.94.25.14025)
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 14025-14030
-
-
Dewji, N.1
Singer, S.J.2
-
8
-
-
0027497369
-
Modeling alpha-helical transmembrane domains: The calculation and use of substitution tables for lipid facing residues
-
Donnelly, D., Overington, J. P., Ruffle, S. V., Nugent, J. & Blundel, T. L. 1993 Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid facing residues. Protein Sci. 2, 55-70.
-
(1993)
Protein Sci.
, vol.2
, pp. 55-70
-
-
Donnelly, D.1
Overington, J.P.2
Ruffle, S.V.3
Nugent, J.4
Blundel, T.L.5
-
9
-
-
0000929505
-
The hydrophobic moment detects periodicity in the protein hydrophobicity
-
Eisenberg, D., Weiss, R. M. & Terwillger, T. 1984 The hydrophobic moment detects periodicity in the protein hydrophobicity. Proc. Natl Acad. Sci. USA 81, 140-144.
-
(1984)
Proc. Natl. Acad. Sci. USA
, vol.81
, pp. 140-144
-
-
Eisenberg, D.1
Weiss, R.M.2
Terwillger, T.3
-
10
-
-
0036382758
-
A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices
-
doi:10.1016/S0022-2836(02)00590-9
-
Fleishman, S. J. & Ben-Tal, N. 2002 A novel scoring function for predicting the conformations of tightly packed pairs of transmembrane alpha-helices. J. Mol. Biol. 321, 363-378. (doi:10.1016/S0022-2836(02)00590-9)
-
(2002)
J. Mol. Biol.
, vol.321
, pp. 363-378
-
-
Fleishman, S.J.1
Ben-Tal, N.2
-
11
-
-
0001008704
-
Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases
-
doi:10.1021/j100133a034
-
Heller, H., Schaefer, M. & Schulten, K. 1993 Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid-crystal phases. J. Phys. Chem. 97, 8343-8360. (doi:10.1021/j100133a034)
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 8343-8360
-
-
Heller, H.1
Schaefer, M.2
Schulten, K.3
-
12
-
-
0031298075
-
Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs
-
doi:10.1002/(SICI)1097-0134(1997) 1 + 〈185::AID-PROT24〉 3.0.CO;2-J
-
Jones, D. T. 1997 Successful ab initio prediction of the tertiary structure of NK-Lysin using multiple sequences and recognized supersecondary structural motifs. Proteins-Suppl. 1, 185-191. (doi:10.1002/(SICI)1097- 0134(1997) 1 + 〈185::AID-PROT24〉 3.0.CO;2-J)
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 185-191
-
-
Jones, D.T.1
-
13
-
-
0032570779
-
Do transmembrane protein superfolds exist?
-
doi:10.1016/S0014-5793 (98)00095-7
-
Jones, D. 1998 Do transmembrane protein superfolds exist? FEBS Lett. 423, 281-285. (doi:10.1016/S0014-5793 (98)00095-7)
-
(1998)
FEBS Lett.
, vol.423
, pp. 281-285
-
-
Jones, D.1
-
14
-
-
0028211273
-
A model recognition approach to the prediction of all-helical membrane protein structure and topology
-
doi:10.1021/bi00176a037
-
Jones, D. T., Taylor, W. R. & Thornton, J. M. 1994 A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33, 3038-3049. (doi:10.1021/bi00176a037)
-
(1994)
Biochemistry
, vol.33
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
15
-
-
0042121119
-
Static benchmarking of membrane helix predictions
-
doi:10.1093/nar/gkg532
-
Kernytsky, A. & Rost, B. 2003 Static benchmarking of membrane helix predictions. Nucleic Acids Res. 31, 3642-3644. (doi:10.1093/nar/gkg532)
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3642-3644
-
-
Kernytsky, A.1
Rost, B.2
-
16
-
-
0029960038
-
Reinitiation of protein translocation across the endoplasmic reticulum membrane for the topogenesis of multi-spanning membrane proteins
-
doi:10.1074/jbc.271.11.6423
-
Kuroiwa, T., Sakaguchi, M., Omura, T. & Mihara, K. 1996 Reinitiation of protein translocation across the endoplasmic reticulum membrane for the topogenesis of multi-spanning membrane proteins. J. Biol. Chem. 271, 6423-6428. (doi:10.1074/jbc.271.11.6423)
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 6423-6428
-
-
Kuroiwa, T.1
Sakaguchi, M.2
Omura, T.3
Mihara, K.4
-
17
-
-
0020475449
-
A simple method for displaying the hydrophathic character of proteins
-
doi:10.1016/0022-2836(82) 90515-0
-
Kyte, J. & Doolittle, R. F. 1982 A simple method for displaying the hydrophathic character of proteins. J. Mol. Biol. 157, 105-132. (doi:10.1016/0022-2836(82) 90515-0)
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
18
-
-
0036962430
-
Modeling the transmembrane arrangement of the uncoupling protein UCP1 and topological considerations of the nucleotide-binding site
-
doi:10.1023/A:1022522310279
-
Ledesma, A., de Lacoba, M. G., Arechaga, I. & Rial, E. 2002 Modeling the transmembrane arrangement of the uncoupling protein UCP1 and topological considerations of the nucleotide-binding site. J Bioenerg. Biomembr. 34, 473-486. (doi:10.1023/A:1022522310279)
-
(2002)
J. Bioenerg. Biomembr.
, vol.34
, pp. 473-486
-
-
Ledesma, A.1
De Lacoba, M.G.2
Arechaga, I.3
Rial, E.4
-
19
-
-
33845312141
-
Analysis of membrane protein families: Genomic prevalence and conserved motifs
-
Liu, Y., Engelman, D. & Gerstein, M. 2002 Analysis of membrane protein families: genomic prevalence and conserved motifs. Genome Biol. 3, 00 054.1-00 054.12.
-
(2002)
Genome Biol.
, vol.3
-
-
Liu, Y.1
Engelman, D.2
Gerstein, M.3
-
20
-
-
0344406716
-
Reliability measures for membrane protein topology prediction algorithms
-
doi:10.1016/S0022-2836(03)00182-7
-
Melen, K., Krogh, A. & von Heijne, G. 2003 Reliability measures for membrane protein topology prediction algorithms. J. Mol. Biol. 327, 735-744. (doi:10.1016/S0022-2836(03)00182-7)
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 735-744
-
-
Melen, K.1
Krogh, A.2
Von Heijne, G.3
-
21
-
-
13444282474
-
InterPro, progress and status in 2005
-
doi:10.1093/nar/gki106
-
Mulder, N. J. 2005 InterPro, progress and status in 2005. Nucleic Acids Res. 33, D201-D205. (doi:10.1093/nar/gki106)
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Mulder, N.J.1
-
22
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
doi:10.1006/jmbi.1995.0159
-
Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. 1995 SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540. (doi:10.1006/jmbi.1995. 0159)
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
23
-
-
0035237770
-
Novel approach to computer modeling of seven-helical case of bactriorhodopsin
-
Nikiforovich, G. V., Galaktionov, S. & Marshal, G. R. 2001 Novel approach to computer modeling of seven-helical case of bactriorhodopsin. Acta Biochim. 48, 53-64.
-
(2001)
Acta Biochim.
, vol.48
, pp. 53-64
-
-
Nikiforovich, G.V.1
Galaktionov, S.2
Marshal, G.R.3
-
24
-
-
0036891703
-
Prediction of partial membrane protein topologies using a consensus approach
-
doi:10.1110/ps.0226702
-
Nilsson, J., Person, B. & von Heijne, G. 2002 Prediction of partial membrane protein topologies using a consensus approach. Protein Sci. 11, 2974-2980. (doi:10.1110/ps.0226702)
-
(2002)
Protein Sci.
, vol.11
, pp. 2974-2980
-
-
Nilsson, J.1
Person, B.2
Von Heijne, G.3
-
25
-
-
0030777303
-
CATH-A hierarchic classification of protein domain structures
-
doi:10.1016/S0969-2126(97) 00260-8
-
Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B. & Thornton, J. M. 1997 CATH-A hierarchic classification of protein domain structures. Structure 5, 1093-1108. (doi:10.1016/S0969-2126(97) 00260-8)
-
(1997)
Structure
, vol.5
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
26
-
-
0029987862
-
Energy functions that discriminate X-ray and near native folds from well-constructed decoys
-
doi:10.1006/jmbi.1996.0256
-
Park, B. & Levitt, M. 1996 Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258, 367-392. (doi:10.1006/jmbi.1996.0256)
-
(1996)
J. Mol. Biol.
, vol.258
, pp. 367-392
-
-
Park, B.1
Levitt, M.2
-
27
-
-
0037339521
-
Folding in lipid membranes (FILM): A novel method for the prediction of small membrane protein 3-D structures
-
doi:10.1002/prot.10304
-
Pellegrini-Calace, M., Carotti, A. & Jones, D. T. 2003 Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3-D structures. Proteins: Struct. Funct. Genet. 50, 537-545. (doi:10.1002/prot.10304)
-
(2003)
Proteins: Struct. Funct. Genet.
, vol.50
, pp. 537-545
-
-
Pellegrini-Calace, M.1
Carotti, A.2
Jones, D.T.3
-
28
-
-
0033544689
-
kPROT: A knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction
-
doi:10.1006/jmbi.1999.3257
-
Pilpel, Y., Ben-Tal, N. & Lancet, D. 1999 kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. J. Mol. Biol. 294, 921-935. (doi:10.1006/jmbi.1999.3257)
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 921-935
-
-
Pilpel, Y.1
Ben-Tal, N.2
Lancet, D.3
-
29
-
-
0025249842
-
Membrane protein folding and oligomerization: The two-stage model
-
doi:10.1021/bi00469a001
-
Popot, J.-L. & Engleman, D. M. 1990 Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29, 4031-4037. (doi:10.1021/bi00469a001)
-
(1990)
Biochemistry
, vol.29
, pp. 4031-4037
-
-
Popot, J.-L.1
Engleman, D.M.2
-
30
-
-
0033790343
-
Helical membrane protein folding, stability, and evolution
-
doi:10.1146/annurev.biochem. 69.1.881
-
Popot, J.-L. & Engleman, D. M. 2000 Helical membrane protein folding, stability, and evolution. Annu. Rev. Biochem. 69, 881-922. (doi:10.1146/ annurev.biochem. 69.1.881)
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 881-922
-
-
Popot, J.-L.1
Engleman, D.M.2
-
31
-
-
0034141371
-
Turning a reference Inside-out: Commentary on an article by Stevens and Arkin Entitled: Are membrane proteins 'inside-out' proteins?
-
doi: 10.1002/(SICI) 1097-0134 (20000201)38:2 〈121::AID-PROT1〉 3.0.CO;2-M
-
Rees, D. C. & Eisenberg, D. 2000 Turning a reference Inside-out: commentary on an article by Stevens and Arkin Entitled: are membrane proteins 'inside-out' proteins? Proteins 38, 121-122. (doi: 10.1002/(SICI) 1097-0134 (20000201)38:2 〈121::AID-PROT1〉 3.0.CO;2-M)
-
(2000)
Proteins
, vol.38
, pp. 121-122
-
-
Rees, D.C.1
Eisenberg, D.2
-
32
-
-
0024346677
-
Hyrophobic organization of membrane proteins
-
Rees, D. C., DeAntonio, L. & Eisenberg, D. 1989 Hyrophobic organization of membrane proteins. Science 245, 510-513.
-
(1989)
Science
, vol.245
, pp. 510-513
-
-
Rees, D.C.1
DeAntonio, L.2
Eisenberg, D.3
-
33
-
-
33845304472
-
Topology prediction for helical transmembrane proteins at 86% accuracy
-
Rost, B., Casadio, R. & Fariselli, P. 1996 Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 4, 521-533.
-
(1996)
Protein Sci.
, vol.4
, pp. 521-533
-
-
Rost, B.1
Casadio, R.2
Fariselli, P.3
-
34
-
-
0031716791
-
Architecture of {beta}-barrel membrane proteins: Analysis of trimeric porin
-
Seshadri, K., Garemyr, R., Walling, E., von Heijne, G. & Elofsson, A. 1998 Architecture of {beta}-barrel membrane proteins: analysis of trimeric porin. Protein Sci. 7, 2026-2032.
-
(1998)
Protein Sci.
, vol.7
, pp. 2026-2032
-
-
Seshadri, K.1
Garemyr, R.2
Walling, E.3
Von Heijne, G.4
Elofsson, A.5
-
35
-
-
0025224551
-
The structure and insertion of integral proteins in membranes
-
Singer, S. J. 1990 The structure and insertion of integral proteins in membranes. Ann. Rev. Cell Biol. 6, 247-296.
-
(1990)
Ann. Rev. Cell Biol.
, vol.6
, pp. 247-296
-
-
Singer, S.J.1
-
36
-
-
0030925920
-
Pfam: A comprehensive database of protein families based on seed alignments
-
doi:10.1002/(SICI) 1097-0134(199707)28:3 〈405::AID-PROT10〉 3.0.CO; 2-L
-
Sonnhammer, E. L., Eddy, S. R. & Durbin, R. 1997 Pfam: a comprehensive database of protein families based on seed alignments. Proteins 28, 405-420. (doi:10.1002/(SICI) 1097-0134(199707)28:3 〈405::AID- PROT10〉 3.0.CO; 2-L)
-
(1997)
Proteins
, vol.28
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
37
-
-
0031614678
-
A hidden Markov model for predicting transmembrane helices in protein sequences
-
Sonnhammer, E. L. et al. 1998 A hidden Markov model for predicting transmembrane helices in protein sequences. Intell. Syst. Mol. Biol. 6, 175-182.
-
(1998)
Intell. Syst. Mol. Biol.
, vol.6
, pp. 175-182
-
-
Sonnhammer, E.L.1
-
38
-
-
0033167996
-
Are membrane proteins 'inside-out' proteins?
-
doi:10.1002/(SICI)1097-0134(19990701)36: 1 〈135::AID-PROT11〉 3.0.CO;2-I
-
Stevens, T. & Arkin, I. T. 1999 Are membrane proteins 'inside-out' proteins? Proteins Struct. Funct. Genet. 36, 135-143. (doi:10.1002/(SICI)1097- 0134(19990701)36: 1 〈135::AID-PROT11〉 3.0.CO;2-I)
-
(1999)
Proteins Struct. Funct. Genet.
, vol.36
, pp. 135-143
-
-
Stevens, T.1
Arkin, I.T.2
-
39
-
-
0028175436
-
A method for alpha-helical integral membrane protein fold prediction
-
doi: 10.1002/prot.340180309
-
Taylor, W. R., Jones, D. T. & Green, N. 1994 A method for alpha-helical integral membrane protein fold prediction. Proteins 18, 281-294. (doi: 10.1002/prot.340180309)
-
(1994)
Proteins
, vol.18
, pp. 281-294
-
-
Taylor, W.R.1
Jones, D.T.2
Green, N.3
-
40
-
-
0032561132
-
Principles governing amino acid composition of integral membrane proteins: Application to topology prediction
-
doi:10.1006/jmbi.1998.2107
-
Tusnady, G. E. & Simon, I. 1998 Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283, 489-506. (doi:10.1006/jmbi.1998.2107)
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 489-506
-
-
Tusnady, G.E.1
Simon, I.2
-
41
-
-
0034057802
-
Membrane topology and insertion of membrane proteins: Search for topogenic signals
-
doi:10.1128/MMBR.64.1.13-33.2000
-
van Geest, M. & Lolkema, J. 2000 Membrane topology and insertion of membrane proteins: search for topogenic signals. Microbiol. Mol. Biol. Rev. 64, 13-33. (doi:10.1128/MMBR.64.1.13-33.2000)
-
(2000)
Microbiol. Mol. Biol. Rev.
, vol.64
, pp. 13-33
-
-
Van Geest, M.1
Lolkema, J.2
-
42
-
-
0026716643
-
Membrane protein structure prediction
-
doi: 10.1016/0022-2836 (92)90934-C
-
von Heijne, G. 1992 Membrane protein structure prediction. J. Mol. Biol. 255, 487-494. (doi: 10.1016/0022-2836 (92)90934-C)
-
(1992)
J. Mol. Biol.
, vol.255
, pp. 487-494
-
-
Von Heijne, G.1
-
43
-
-
0030431744
-
Principles of membrane protein assembly and structure
-
doi:10.1016/S0079-6107(97)85627-1
-
von Heijne, G. 1996 Principles of membrane protein assembly and structure. Progr. Biophys. Mol. Biol. 66, 113-139. (doi:10.1016/S0079-6107(97) 85627-1)
-
(1996)
Progr. Biophys. Mol. Biol.
, vol.66
, pp. 113-139
-
-
Von Heijne, G.1
-
44
-
-
0033342531
-
Recent advances in the understanding of membrane protein assembly and structure
-
doi:10.1017/S00335835 00003541
-
von Heijne, G. 1999 Recent advances in the understanding of membrane protein assembly and structure. Quart. Rev. Biophys. 32, 285-307. (doi:10.1017/S00335835 00003541)
-
(1999)
Quart. Rev. Biophys.
, vol.32
, pp. 285-307
-
-
Von Heijne, G.1
-
45
-
-
0031954925
-
Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms
-
Wallin, E. & von Heijne, G. 1998 Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7, 1029-1038.
-
(1998)
Protein Sci.
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
46
-
-
0035980121
-
How membranes shape protein structure
-
doi:10.1074/jbc. R100008200
-
White, S. H. 2001 How membranes shape protein structure. J. Biol. Chem. 31, 32395-32398. (doi:10.1074/jbc. R100008200)
-
(2001)
J. Biol. Chem.
, vol.31
, pp. 32395-32398
-
-
White, S.H.1
-
47
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
doi:10.1146/annurev. biophys.28.1.319
-
White, S. H. & Wimley, W. C. 1999 Membrane protein folding and stability: physical principles. Annu. Rev. Biophys. Struct. 28, 319-365. (doi:10.1146/annurev. biophys.28.1.319)
-
(1999)
Annu. Rev. Biophys. Struct.
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
|