-
1
-
-
0031584266
-
Potein evolution viewed through Escherichua coli protein sequences: Introducing the notion of a structural segment of homology, the module
-
Riley M., Labedan B. Potein evolution viewed through Escherichua coli protein sequences: introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268:1997;857-868
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 857-868
-
-
Riley, M.1
Labedan, B.2
-
2
-
-
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. 299:2000;897-905
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 897-905
-
-
Wolf, Y.I.1
Grishin, N.V.2
Koonin, E.V.3
-
3
-
-
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. 420:2002;218-223
-
(2002)
Nature
, vol.420
, pp. 218-223
-
-
Koonin, E.V.1
Wolf, Y.I.2
Karev, G.P.3
-
5
-
-
0036084625
-
SCOP database in 2002: Refinements accommodate structural genomics
-
Lo Conte L., Brenner S.E., Hubbard T.J., Chothia C., Murzin A.G. SCOP database in 2002: refinements accommodate structural genomics. Nucl. Acids Res. 30:2002;264-267
-
(2002)
Nucl. Acids Res.
, vol.30
, pp. 264-267
-
-
Lo Conte, L.1
Brenner, S.E.2
Hubbard, T.J.3
Chothia, C.4
Murzin, A.G.5
-
6
-
-
0033985050
-
Assigning genomic sequences to CATH
-
Pearl F.M., Lee D., Bray J.E., Sillitoe I., Todd A.E., Harrison A.P., et al. Assigning genomic sequences to CATH. Nucl. Acids Res. 28:2000;277-282
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 277-282
-
-
Pearl, F.M.1
Lee, D.2
Bray, J.E.3
Sillitoe, I.4
Todd, A.E.5
Harrison, A.P.6
-
7
-
-
0032424307
-
Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements
-
Teichmann S.A., Park J., Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl Acid. Sci. USA. 9:1998;14658-14663
-
(1998)
Proc. Natl Acid. Sci. USA
, vol.9
, pp. 14658-14663
-
-
Teichmann, S.A.1
Park, J.2
Chothia, C.3
-
9
-
-
0032570779
-
Do transmembrane protein superfolds exist?
-
Jones D.T. Do transmembrane protein superfolds exist? FEBS Letters. 423:1998;281-285
-
(1998)
FEBS Letters
, vol.423
, pp. 281-285
-
-
Jones, D.T.1
-
10
-
-
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. 7:1998;1029-1038
-
(1998)
Protein Sci.
, vol.7
, pp. 1029-1038
-
-
Wallin, E.1
Von Heijne, G.2
-
11
-
-
0032834939
-
An hierarchical artificial neural network system for the classification of transmembrane proteins
-
Pasquier C., Hamodrakas S.J. An hierarchical artificial neural network system for the classification of transmembrane proteins. Protein Eng. 12:1999;631-634
-
(1999)
Protein Eng.
, vol.12
, pp. 631-634
-
-
Pasquier, C.1
Hamodrakas, S.J.2
-
12
-
-
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. 82:1999;165-171
-
(1999)
Biophys. Chem.
, vol.82
, pp. 165-171
-
-
Mitaku, S.1
Ono, M.2
Hirokawa, T.3
Boon-Chieng, S.4
Sonoyama, M.5
-
13
-
-
0034213573
-
Do more complex organisms have a greater proportion of membrane proteins in their genomes?
-
Stevens T.J., Arkin I.T. Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins: Struct. Funct. Genet. 39:2000;417-420
-
(2000)
Proteins: Struct. Funct. Genet.
, vol.39
, pp. 417-420
-
-
Stevens, T.J.1
Arkin, I.T.2
-
14
-
-
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. 305:2001;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
-
15
-
-
0034808117
-
Comparing function and structure between entire proteomes
-
Liu J., Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10:2001;1970-1979
-
(2001)
Protein Sci.
, vol.10
, pp. 1970-1979
-
-
Liu, J.1
Rost, B.2
-
16
-
-
0037472764
-
Comprehensive analysis of transmembrane topologies in prokaryotic genomes
-
Arai M., Ikeda M., Shimizu T. Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene. 304:2003;77-86
-
(2003)
Gene
, vol.304
, pp. 77-86
-
-
Arai, M.1
Ikeda, M.2
Shimizu, T.3
-
17
-
-
0035379645
-
2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies
-
2+ exchanger-related Escherichia coli protein YrbG have opposite membrane topologies. J. Biol. Chem. 276:2001;18905-18907
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 18905-18907
-
-
Sääf, A.1
Baars, L.2
Von Heijne, G.3
-
18
-
-
0030309453
-
Phylogenetic approaches to the identification and characterization of protein families and superfamilies
-
Saier M.H. Jr. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. Microb. Comp. Genomics. 1:1996;129-150
-
(1996)
Microb. Comp. Genomics
, vol.1
, pp. 129-150
-
-
Saier Jr., M.H.1
-
19
-
-
0033821267
-
Vectorial metabolism and the evolution of transport systems
-
Saier M.H. Jr. Vectorial metabolism and the evolution of transport systems. J. Bacteriol. 182:2000;5029-5035
-
(2000)
J. Bacteriol.
, vol.182
, pp. 5029-5035
-
-
Saier Jr., M.H.1
-
20
-
-
0037783318
-
Tracing pathways of transport protein evolution
-
Saier M.H. Jr. Tracing pathways of transport protein evolution. Mol. Microbiol. 48:2003;1145-1156
-
(2003)
Mol. Microbiol.
, vol.48
, pp. 1145-1156
-
-
Saier Jr., M.H.1
-
21
-
-
0041353145
-
Structure and mechanism of the lactose permease of Escherichia coli
-
Abramson J., Smirnova I., Kasho V., Verner G., Kaback H.R., Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science. 301:2003;610-615
-
(2003)
Science
, vol.301
, pp. 610-615
-
-
Abramson, J.1
Smirnova, I.2
Kasho, V.3
Verner, G.4
Kaback, H.R.5
Iwata, S.6
-
22
-
-
0242497235
-
Structure of mitochondrial ADP/ATP carrier in complex with carboxyatratyloside
-
Pebay-Peyroula E., Dahout-Gonzalez C., Kahn R., Trezeguet V., Lauquin G.J., Brandolin G. Structure of mitochondrial ADP/ATP carrier in complex with carboxyatratyloside. Nature. 426:2003;39-44
-
(2003)
Nature
, vol.426
, pp. 39-44
-
-
Pebay-Peyroula, E.1
Dahout-Gonzalez, C.2
Kahn, R.3
Trezeguet, V.4
Lauquin, G.J.5
Brandolin, G.6
-
23
-
-
0027193530
-
Sequence homology between bacteriorhodopsin and G-protein coupled receptors: Exon shuffling or evolution by duplication?
-
Taylor E.W., Agarwal A. Sequence homology between bacteriorhodopsin and G-protein coupled receptors: exon shuffling or evolution by duplication? FEBS Letters. 325:1993;161-166
-
(1993)
FEBS Letters
, vol.325
, pp. 161-166
-
-
Taylor, E.W.1
Agarwal, A.2
-
24
-
-
0035795114
-
Homologues of archaeal rhodopsins in plants, animals and fungi: Structural and functional predictions for a putative fungal chaperone protein
-
Zhai Y., Heijne W.H., Smith D.W., Saier M.H. Jr. Homologues of archaeal rhodopsins in plants, animals and fungi: structural and functional predictions for a putative fungal chaperone protein. Biochim. Biophys. Acta. 1511:2001;206-223
-
(2001)
Biochim. Biophys. Acta
, vol.1511
, pp. 206-223
-
-
Zhai, Y.1
Heijne, W.H.2
Smith, D.W.3
Saier Jr., M.H.4
-
25
-
-
0024442722
-
Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues
-
von Heijne G. Control of topology and mode of assembly of a polytopic membrane protein by positively charged residues. Nature. 341:1989;456-458
-
(1989)
Nature
, vol.341
, pp. 456-458
-
-
Von Heijne, G.1
-
26
-
-
0023676242
-
Topogenic signals in integral membrane proteins
-
von Heijne G., Gavel Y. Topogenic signals in integral membrane proteins. Eur. J. Biochem. 174:1988;671-678
-
(1988)
Eur. J. Biochem.
, vol.174
, pp. 671-678
-
-
Von Heijne, G.1
Gavel, Y.2
-
27
-
-
0027264995
-
Predicting the topology of eukaryotic membrane proteins
-
Sipos L., von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213:1993;1333-1340
-
(1993)
Eur. J. Biochem.
, vol.213
, pp. 1333-1340
-
-
Sipos, L.1
Von Heijne, G.2
-
28
-
-
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. 2:2002;19-33
-
(2002)
In Silico Biol.
, vol.2
, pp. 19-33
-
-
Ikeda, M.1
Arai, M.2
Lao, D.M.3
Shimizu, T.4
-
29
-
-
0037249645
-
TMPDB: A database of experimentally-characterized transmembrane topologies
-
Ikeda M., Arai M., Shimizu T. TMPDB: a database of experimentally- characterized transmembrane topologies. Nucl. Acids Res. 31:2003;406-409
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 406-409
-
-
Ikeda, M.1
Arai, M.2
Shimizu, T.3
-
30
-
-
0033587738
-
Divergent evolution of membrane protein topology: The Escherichia coli RnfA and RnfE homologues
-
Sääf A., Johansson M., Wallin E., von Heijne G. Divergent evolution of membrane protein topology: the Escherichia coli RnfA and RnfE homologues. Proc. Natl Acad. Sci. USA. 96:1999;8540-8544
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 8540-8544
-
-
Sääf, A.1
Johansson, M.2
Wallin, E.3
Von Heijne, G.4
-
31
-
-
0042880963
-
Identification of transmembrane protein functions by binary topology patterns
-
Sugiyama Y., Polulyakh N., Shimizu T. Identification of transmembrane protein functions by binary topology patterns. Protein Eng. 16:2003;479-488
-
(2003)
Protein Eng.
, vol.16
, pp. 479-488
-
-
Sugiyama, Y.1
Polulyakh, N.2
Shimizu, T.3
-
32
-
-
0037245984
-
GenBank
-
Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucl. Acids Res. 31:2003;23-27
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 23-27
-
-
Benson, D.A.1
Karsch-Mizrachi, I.2
Lipman, D.J.3
Ostell, J.4
Wheeler, D.L.5
-
33
-
-
0031826040
-
SOSUI: Classification and secondary structure prediction system for membrane proteins
-
Hirokawa T., Boon-Chieng S., Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 14:1998;378-379
-
(1998)
Bioinformatics
, vol.14
, pp. 378-379
-
-
Hirokawa, T.1
Boon-Chieng, S.2
Mitaku, S.3
-
35
-
-
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. 18:2002;1562-1566
-
(2002)
Bioinformatics
, vol.18
, pp. 1562-1566
-
-
Lao, D.M.1
Arai, M.2
Ikeda, M.3
Shimizu, T.4
-
36
-
-
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. 2:2002;485-494
-
(2002)
In Silico Biol.
, vol.2
, pp. 485-494
-
-
Lao, D.M.1
Okuno, T.2
Shimizu, T.3
-
37
-
-
0021847027
-
The detection and classification of membrane-spanning proteins
-
Klein P., Kanehisa M., DeLisi C. The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta. 815:1985;468-476
-
(1985)
Biochim. Biophys. Acta
, vol.815
, pp. 468-476
-
-
Klein, P.1
Kanehisa, M.2
Delisi, C.3
-
38
-
-
0028568176
-
TopPred II: An improved software for membrane protein structure predictions
-
Claros M.G., von Heijne G. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10:1994;685-686
-
(1994)
Comput. Appl. Biosci.
, vol.10
, pp. 685-686
-
-
Claros, M.G.1
Von Heijne, G.2
-
39
-
-
53249092142
-
Prediction of membrane protein topology utilizing multiple sequence alignments
-
Persson B., Argos P. Prediction of membrane protein topology utilizing multiple sequence alignments. J. Protein Chem. 16:1997;453-457
-
(1997)
J. Protein Chem.
, vol.16
, pp. 453-457
-
-
Persson, B.1
Argos, P.2
-
40
-
-
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. 33:1994;3038-3049
-
(1994)
Biochemistry
, vol.33
, pp. 3038-3049
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
41
-
-
0031614678
-
A hidden Markov model for predicting transmembrane helices in protein sequences
-
J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, & C. Sensen. Menlo Park, CA: AAAI Press
-
Sonnhammer E.L., von Heijne G., Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Glasgow J., Littlejohn T., Major F., Lathrop R., Sankoff D., Sensen C. Proceedings of Sixth International Conference of Intelligent System for Molecular Biology (ISMB 1998). 1998;175-182 AAAI Press, Menlo Park, CA
-
(1998)
Proceedings of Sixth International Conference of Intelligent System for Molecular Biology (ISMB 1998)
, pp. 175-182
-
-
Sonnhammer, E.L.1
Von Heijne, G.2
Krogh, A.3
-
42
-
-
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. 283:1998;489-506
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 489-506
-
-
Tusnády, G.E.1
Simon, I.2
-
43
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnády G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:2001;849-850
-
(2001)
Bioinformatics
, vol.17
, pp. 849-850
-
-
Tusnády, G.E.1
Simon, I.2
-
44
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402
-
(1997)
Nucl. Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
46
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson W.R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics. 11:1991;635-650
-
(1991)
Genomics
, vol.11
, pp. 635-650
-
-
Pearson, W.R.1
-
47
-
-
0037255072
-
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003
-
Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucl. Acids Res. 31:2003;365-370
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 365-370
-
-
Boeckmann, B.1
Bairoch, A.2
Apweiler, R.3
Blatter, M.C.4
Estreicher, A.5
Gasteiger, E.6
|