-
2
-
-
0037376703
-
Global approaches to protein-protein interactions
-
Drewes G, Bouwmeester T: Global approaches to protein-protein interactions. Curr Opin Cell Biol 2003, 15: 199-205.
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 199-205
-
-
Drewes, G.1
Bouwmeester, T.2
-
3
-
-
0031734751
-
Comparing genomes in terms of protein structure: Surveys of a finite parts list
-
Gerstein M, Hegyi H: Comparing genomes in terms of protein structure: surveys of a finite parts list. FEMS Microbiol Rev 1998, 22: 277-304.
-
(1998)
FEMS Microbiol. Rev.
, vol.22
, pp. 277-304
-
-
Gerstein, M.1
Hegyi, H.2
-
4
-
-
0029979607
-
Common principles of protein translocation across membranes
-
Schatz G, Dobberstein B: Common principles of protein translocation across membranes. Science 1996, 271: 1519-1526.
-
(1996)
Science
, vol.271
, pp. 1519-1526
-
-
Schatz, G.1
Dobberstein, B.2
-
6
-
-
0141746356
-
LumenP - A neural network predictor for protein localization in the thylakoid lumen
-
Westerlund I, von Heijne, G, Emanuelsson O: LumenP - a neural network predictor for protein localization in the thylakoid lumen. Protein Sci 2003, 12: 2360-2366.
-
(2003)
Protein Sci.
, vol.12
, pp. 2360-2366
-
-
Westerlund, I.1
von Heijne, G.2
Emanuelsson, O.3
-
7
-
-
0034899781
-
Evaluation of methods for the prediction of membrane spanning regions
-
Möller S, Croning MD, Apweiler R: Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 2001, 17: 646-653.
-
(2001)
Bioinformatics
, vol.17
, pp. 646-653
-
-
Möller, S.1
Croning, M.D.2
Apweiler, R.3
-
8
-
-
0344406716
-
Reliability measures for membrane protein topology prediction algorithms
-
Melen K, Krogh A, von Heijne G: Reliability measures for membrane protein topology prediction algorithms. J Mol Biol 2003, 327: 735-744.
-
(2003)
J. Mol. Biol.
, vol.327
, pp. 735-744
-
-
Melen, K.1
Krogh, A.2
von Heijne, G.3
-
9
-
-
0035078840
-
Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor
-
Jacoboni I, Martelli PL, Fariselli P, De Pinto V, Casadio R: Prediction of the transmembrane regions of beta-barrel membrane proteins with a neural network-based predictor. Protein Sci 2001, 10: 779-787.
-
(2001)
Protein Sci.
, vol.10
, pp. 779-787
-
-
Jacoboni, I.1
Martelli, P.L.2
Fariselli, P.3
De Pinto, V.4
Casadio, R.5
-
10
-
-
4243671284
-
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins
-
Martelli PL, Fariselli P, Krogh A, Casadio R: A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics 2002, 18 Suppl 1: 46-53.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
, pp. 46-53
-
-
Martelli, P.L.1
Fariselli, P.2
Krogh, A.3
Casadio, R.4
-
11
-
-
3042678854
-
Predicting transmembrane beta-barrels in proteomes
-
Bigelow HR, Petrey DS, Liu J, Przybylski D, Rost B: Predicting transmembrane beta-barrels in proteomes. Nucleic Acids Res 2004, 32: 2566-2577.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 2566-2577
-
-
Bigelow, H.R.1
Petrey, D.S.2
Liu, J.3
Przybylski, D.4
Rost, B.5
-
12
-
-
2942522711
-
A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins
-
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamdrakas SJ: A Hidden Markov Model method, capable of predicting and discriminating β-barrel outer membrane proteins. BMC Bioinformatics 2004, 5: 29.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 29
-
-
Bagos, P.G.1
Liakopoulos, T.D.2
Spyropoulos, I.C.3
Hamdrakas, S.J.4
-
13
-
-
0036708003
-
The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes
-
Zhai Y, Saier MH Jr: The beta-barrel finder (BBF) program, allowing identification of outer membrane beta-barrel proteins encoded within prokaryotic genomes. Protein Sci 2002, 11: 2196-2207.
-
(2002)
Protein Sci.
, vol.11
, pp. 2196-2207
-
-
Zhai, Y.1
Saier Jr., M.H.2
-
14
-
-
0036147641
-
Toward genomic identification of beta-barrel membrane proteins: Composition and architecture of known structures
-
Wimley WC: Toward genomic identification of beta-barrel membrane proteins: composition and architecture of known structures. Protein Sci 2002, 11: 301-312.
-
(2002)
Protein Sci.
, vol.11
, pp. 301-312
-
-
Wimley, W.C.1
-
15
-
-
0037379183
-
Prediction of the plant beta-barrel proteome: A case study of the chloroplast outer envelope
-
Schleiff E, Eichacker LA, Eckart K, Becker T, Mirus O, Stahl T, Soll J: Prediction of the plant beta-barrel proteome: a case study of the chloroplast outer envelope. Protein Sci 2003, 12: 748-759.
-
(2003)
Protein Sci.
, vol.12
, pp. 748-759
-
-
Schleiff, E.1
Eichacker, L.A.2
Eckart, K.3
Becker, T.4
Mirus, O.5
Stahl, T.6
Soll, J.7
-
16
-
-
23144440152
-
TMB-Hunt: A web server to screen sequence sets for transmembrane beta-barrel proteins
-
Garrow AG, Agnew A, Westhead DR: TMB-Hunt: a web server to screen sequence sets for transmembrane beta-barrel proteins. Nucleic Acids Res. 2005, 33: W188-192.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Garrow, A.G.1
Agnew, A.2
Westhead, D.R.3
-
17
-
-
25444484398
-
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
-
Garrow AG, Agnew A, Westhead DR. TMB-Hunt: an amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins. BMC Bioinformatics 2005, 6: 56.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 56
-
-
Garrow, A.G.1
Agnew, A.2
Westhead, D.R.3
-
18
-
-
23944452881
-
Proteomic analysis of the Outer Membrane of Anabaena sp. Strain PCC 7120
-
Moslavac S, Bredemeier R, Mirus O, Granvogl B., Eichacker LA, Schleiff E: Proteomic analysis of the Outer Membrane of Anabaena sp. Strain PCC 7120. J Prot Res 2005, 4: 1330-1338.
-
(2005)
J. Prot. Res.
, vol.4
, pp. 1330-1338
-
-
Moslavac, S.1
Bredemeier, R.2
Mirus, O.3
Granvogl, B.4
Eichacker, L.A.5
Schleiff, E.6
-
19
-
-
3242879514
-
BOMP: A program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria
-
Berven FS, Flikka K, Jensen HB, Eidhammer I: BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. Nucleic Acids Res 2004, 32: W394-399.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Berven, F.S.1
Flikka, K.2
Jensen, H.B.3
Eidhammer, I.4
-
20
-
-
0027092678
-
Selection of representative protein data sets
-
Hobohm U, Scharf M, Schneider R, Sander C: Selection of representative protein data sets. Protein Sci 1992, 1: 409-417.
-
(1992)
Protein Sci.
, vol.1
, pp. 409-417
-
-
Hobohm, U.1
Scharf, M.2
Schneider, R.3
Sander, C.4
-
21
-
-
0031829372
-
Removing near-neighbour redundancy from large protein sequence collections
-
Holm L, Sander C: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 1998, 14: 423-429.
-
(1998)
Bioinformatics
, vol.14
, pp. 423-429
-
-
Holm, L.1
Sander, C.2
-
22
-
-
0034951509
-
Optimal classification of protein sequences and selection of representative sets from multiple alignments: Application to homologous families and lessons for structural genomics
-
May ACW: Optimal classification of protein sequences and selection of representative sets from multiple alignments: application to homologous families and lessons for structural genomics. Protein Eng 2001, 14: 209-217.
-
(2001)
Protein Eng.
, vol.14
, pp. 209-217
-
-
May, A.C.W.1
-
23
-
-
3142529119
-
Scoring hidden Markov models to discriminate beta-barrel membrane proteins
-
Deng Y, Liu Q, Li YX: Scoring hidden Markov models to discriminate beta-barrel membrane proteins. Comput Biol Chem 2004, 28: 189-194.
-
(2004)
Comput. Biol. Chem.
, vol.28
, pp. 189-194
-
-
Deng, Y.1
Liu, Q.2
Li, Y.X.3
-
25
-
-
0037064291
-
The structure of bacterial outer membrane proteins
-
Schulz GE: The structure of bacterial outer membrane proteins. Biochim Biophys Acta 2002, 1565: 308-317.
-
(2002)
Biochim. Biophys. Acta
, vol.1565
, pp. 308-317
-
-
Schulz, G.E.1
-
26
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh A, Larsson B, von Heijne G, Sonnhammer EL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305: 567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.4
-
27
-
-
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: 1029-1038.
-
(1998)
Protein Sci.
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
von Heijne, G.2
-
28
-
-
4544346057
-
Structure of the Neisseria meningitides Outer Membrane PilQ Secretin Complex at 12 Å Resolution
-
Collins RF, Frye SA, Kitmitto A, Ford RC, Tønjum T, Derrick JP: Structure of the Neisseria meningitides Outer Membrane PilQ Secretin Complex at 12 Å Resolution. J Bio Chem 2004, 279: 39750-39756.
-
(2004)
J. Bio. Chem.
, vol.279
, pp. 39750-39756
-
-
Collins, R.F.1
Frye, S.A.2
Kitmitto, A.3
Ford, R.C.4
Tønjum, T.5
Derrick, J.P.6
-
29
-
-
0037143630
-
Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters
-
Ferro M, Salvi D, Riviere-Rolland H, Vermat T, Seigneurin-Berny D, Grunwald D, Garin J, Joyard J, Rolland N: Integral membrane proteins of the chloroplast envelope: identification and subcellular localization of new transporters. Proc Natl Acad Sci USA 2002, 99: 11487-11492.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11487-11492
-
-
Ferro, M.1
Salvi, D.2
Riviere-Rolland, H.3
Vermat, T.4
Seigneurin-Berny, D.5
Grunwald, D.6
Garin, J.7
Joyard, J.8
Rolland, N.9
-
30
-
-
0031716791
-
Architecture of beta-barrel membrane proteins: Analysis of trimeric porins
-
Seshadri K, Garemyr R, Wallin E, von Heijne G, Elofsson A: Architecture of beta-barrel membrane proteins: analysis of trimeric porins. Protein Sci 1998, 7: 2026-2032.
-
(1998)
Protein Sci.
, vol.7
, pp. 2026-2032
-
-
Seshadri, K.1
Garemyr, R.2
Wallin, E.3
von Heijne, G.4
Elofsson, A.5
-
32
-
-
16344376554
-
A simple statistical method for discriminating outer membrane proteins with better accuracy
-
Gromiha MM, Suwa M: A simple statistical method for discriminating outer membrane proteins with better accuracy. Bioinformatics 2005, 21: 961-968.
-
(2005)
Bioinformatics
, vol.21
, pp. 961-968
-
-
Gromiha, M.M.1
Suwa, M.2
-
33
-
-
0034730655
-
Novel topological features of FhaC, the outer membrane transporter involved in the secretion of the Bordetella pertussis filamentous hemagglutinin
-
Guedin S, Willery E, Tommassen J, Fort E, Drobecq H, Locht C, Jacob-Dubuisson F: Novel topological features of FhaC, the outer membrane transporter involved in the secretion of the Bordetella pertussis filamentous hemagglutinin. J Biol Chem 2000, 275: 30202-30210.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 30202-30210
-
-
Guedin, S.1
Willery, E.2
Tommassen, J.3
Fort, E.4
Drobecq, H.5
Locht, C.6
Jacob-Dubuisson, F.7
-
34
-
-
0032991297
-
The haemolysin-secreting ShlB protein of the outer membrane of Serratia marcescens: Determination of surface-exposed residues and formation of ion-permeable pores by ShlB mutants in artificial lipid bilayer membranes
-
Könninger UW, Hobbie S, Benz R, Braun V: The haemolysin-secreting ShlB protein of the outer membrane of Serratia marcescens: determination of surface-exposed residues and formation of ion-permeable pores by ShlB mutants in artificial lipid bilayer membranes. Mol Microbiol 1999, 32: 1212-1225.
-
(1999)
Mol. Microbiol.
, vol.32
, pp. 1212-1225
-
-
Könninger, U.W.1
Hobbie, S.2
Benz, R.3
Braun, V.4
-
35
-
-
15944419107
-
Conserved pore-forming regions in polypeptide-transporting proteins
-
Moslavac S, Mirus O, Bredemeier R, Soll J, von Haeseler A, Schleiff E: Conserved pore-forming regions in polypeptide-transporting proteins. FEBS J 2005, 272: 1367-1378.
-
(2005)
FEBS J.
, vol.272
, pp. 1367-1378
-
-
Moslavac, S.1
Mirus, O.2
Bredemeier, R.3
Soll, J.4
von Haeseler, A.5
Schleiff, E.6
-
36
-
-
23344442676
-
The Evolutionary related β-barrel polypeptide transporters from P. sativum and Nostoc PCC7120 contain two distinct functional domains
-
Ertel F, Mirus O, Bredemeier R, Moslavac S, Becker T, Schleiff E: The Evolutionary related β-barrel polypeptide transporters from P. sativum and Nostoc PCC7120 contain two distinct functional domains. J Biol Chem 2005, 280: 28281-28289.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 28281-28289
-
-
Ertel, F.1
Mirus, O.2
Bredemeier, R.3
Moslavac, S.4
Becker, T.5
Schleiff, E.6
-
37
-
-
2342578691
-
Internal gene duplication in the evolution of prokaryotic transmembrane proteins
-
Shimizu T, Mitsuke H, Noto K, Arai M: Internal gene duplication in the evolution of prokaryotic transmembrane proteins. J Mol Biol 2004, 339: 1-15.
-
(2004)
J. Mol. Biol.
, vol.339
, pp. 1-15
-
-
Shimizu, T.1
Mitsuke, H.2
Noto, K.3
Arai, M.4
-
38
-
-
0041428149
-
The versatile beta-barrel membrane protein
-
Wimley WC: The versatile beta-barrel membrane protein. Curr Opin Struct Biol 2003, 13(4): 404-411.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, Issue.4
, pp. 404-411
-
-
Wimley, W.C.1
-
39
-
-
1642446957
-
From the Sequence to Cell Modeling: Comprehensive Functional Genomics in Escherichia coli
-
Mori H: From the Sequence to Cell Modeling: Comprehensive Functional Genomics in Escherichia coli. J Biochem Mol Biol 2004, 37: 83-92.
-
(2004)
J. Biochem. Mol. Biol.
, vol.37
, pp. 83-92
-
-
Mori, H.1
-
40
-
-
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: 406-409.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 406-409
-
-
Ikeda, M.1
Arai, M.2
Okuno, T.3
Shimizu, T.4
-
41
-
-
84874644869
-
-
TMPDB FTP ftp://bioinfo.si.hirosaki-u.ac.jp/TMPDB/Release_6.3/
-
TMPDB FTP [ftp://bioinfo.si.hirosaki-u.ac.jp/TMPDB/Release_6.3/]
-
-
-
-
42
-
-
13444301472
-
PSORTDB: A Database of Subcellular Localizations for Bacteria
-
Rey S, Acab M, Gardy JL, Laird MR, deFays K, Lambert C, Brinkman FSL: PSORTDB: A Database of Subcellular Localizations for Bacteria. Nucleic Acids Res 2005, 33: 164-168.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 164-168
-
-
Rey, S.1
Acab, M.2
Gardy, J.L.3
Laird, M.R.4
deFays, K.5
Lambert, C.6
Brinkman, F.S.L.7
-
43
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28: 235-242.
-
(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
-
44
-
-
84860134058
-
RCSB Protein Data Bank
-
RCSB Protein Data Bank [http://pdbbeta.rcsb.org/pdb]
-
-
-
-
45
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247: 536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
46
-
-
84874659604
-
-
NCBI FTP
-
NCBI FTP
-
-
-
-
47
-
-
0031740601
-
Hydrophobic interactions of peptides with membrane interfaces
-
White SH, Wimley WC: Hydrophobic interactions of peptides with membrane interfaces. Biochim Biophys Acta 1998, 1376: 339-352.
-
(1998)
Biochim. Biophys. Acta
, vol.1376
, pp. 339-352
-
-
White, S.H.1
Wimley, W.C.2
-
48
-
-
84874664833
-
-
TMHMM Server v. 2.0
-
TMHMM Server v. 2.0 [http://www.cbs.dtu.dk/services/TMHMM/]
-
-
-
|