-
1
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol.
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
2
-
-
0037472764
-
Comprehensive analysis of transmembrane topologies in prokaryotic genomes
-
Arai,M., Ikeda,M. and Shimizu,T. (2003) Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene, 304, 77-86.
-
(2003)
Gene
, vol.304
, pp. 77-86
-
-
Arai, M.1
Ikeda, M.2
Shimizu, T.3
-
3
-
-
0033567092
-
Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 Å resolution
-
Belrhali,H., Nollert,P., Royant,A., Menzel,C., Rosenbusch,J.P., Landau,E.M. and Pebay-Peyroula,E. (1999) Protein, lipid and water organization in bacteriorhodopsin crystals: A molecular view of the purple membrane at 1.9 Å resolution. Structure Fold Des., 7, 909-917.
-
(1999)
Structure Fold Des.
, vol.7
, pp. 909-917
-
-
Belrhali, H.1
Nollert, P.2
Royant, A.3
Menzel, C.4
Rosenbusch, J.P.5
Landau, E.M.6
Pebay-Peyroula, E.7
-
4
-
-
0031892162
-
How many membrane proteins are there?
-
Boyd,D., Schierle,C. and Beckwith,J. (1998) How many membrane proteins are there? Protein Sci., 7, 201-205.
-
(1998)
Protein Sci.
, vol.7
, pp. 201-205
-
-
Boyd, D.1
Schierle, C.2
Beckwith, J.3
-
5
-
-
0036893269
-
Transmembrane helix predictions revisited
-
Chen,C.P., Kernytsky,A. and Rost,B. (2002) Transmembrane helix predictions revisited. Protein Sci., 11, 2774-2791.
-
(2002)
Protein Sci.
, vol.11
, pp. 2774-2791
-
-
Chen, C.P.1
Kernytsky, A.2
Rost, B.3
-
6
-
-
0032478818
-
+ conduction and selectivity
-
+ conduction and selectivity. Science, 280, 69-77.
-
(1998)
Science
, vol.280
, pp. 69-77
-
-
Doyle, D.A.1
Morais, C.J.2
Pfuetzner, R.A.3
Kuo, A.4
Gulbis, J.M.5
Cohen, S.L.6
Chait, B.T.7
MacKinnon, R.8
-
7
-
-
0003516147
-
-
Cambridge Press, Cambridge, UK
-
Durbin,R., Eddy,S., Krogh,A. and Mitchison,G. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge Press, Cambridge, UK.
-
(1998)
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
9
-
-
0037083541
-
A study on protein sequence alignment quality
-
Elofsson,A. (2002) A study on protein sequence alignment quality. Proteins, 46, 330-339.
-
(2002)
Proteins
, vol.46
, pp. 330-339
-
-
Elofsson, A.1
-
10
-
-
0037339488
-
MaxSubSeq: An algorithm for segment-length optimization. The case study of the transmembrane spanning segments
-
Fariselli,P., Finelli,M., Marchignoli,D., Martelli,P.L., Rossi,I. and Casadio,R. (2003) MaxSubSeq: An algorithm for segment-length optimization. The case study of the transmembrane spanning segments. Bioinformatics, 19, 500-505.
-
(2003)
Bioinformatics
, vol.19
, pp. 500-505
-
-
Fariselli, P.1
Finelli, M.2
Marchignoli, D.3
Martelli, P.L.4
Rossi, I.5
Casadio, R.6
-
11
-
-
0021977590
-
Amino-acid side-chain partition energies and distribution of residues in soluble-proteins
-
Guy,H.R. (1985) Amino-acid side-chain partition energies and distribution of residues in soluble-proteins. Biophys. J., 47, 61-70.
-
(1985)
Biophys. J.
, vol.47
, pp. 61-70
-
-
Guy, H.R.1
-
12
-
-
0024522057
-
A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites
-
Henneke,C.M. (1989) A multiple sequence alignment algorithm for homologous proteins using secondary structure information and optionally keying alignments to functionally important sites. Comput. Appl. Biosci., 5, 141-150.
-
(1989)
Comput. Appl. Biosci.
, vol.5
, pp. 141-150
-
-
Henneke, C.M.1
-
13
-
-
0037198626
-
Crystal structure and mechanism of a calcium-gated potassium channel
-
Jiang,Y., Lee,A., Chen,J., Cadene,M., Chait,B.T. and MacKinnon,R. (2002) Crystal structure and mechanism of a calcium-gated potassium channel. Nature, 417, 515-522.
-
(2002)
Nature
, vol.417
, pp. 515-522
-
-
Jiang, Y.1
Lee, A.2
Chen, J.3
Cadene, M.4
Chait, B.T.5
MacKinnon, R.6
-
14
-
-
0038076054
-
+ channel
-
+ channel. Nature, 423, 33-41.
-
(2003)
Nature
, vol.423
, pp. 33-41
-
-
Jiang, Y.1
Lee, A.2
Chen, J.3
Ruta, V.4
Cadene, M.5
Chait, B.T.6
MacKinnon, R.7
-
15
-
-
0028153788
-
A mutation data matrix for transmembrane proteins
-
Jones,D.T., Taylor,W.R. and Thornton,J.M. (1994) A mutation data matrix for transmembrane proteins, FEBS Lett., 339, 269-275.
-
(1994)
FEBS Lett.
, vol.339
, pp. 269-275
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
16
-
-
0037132511
-
Reliability of transmembrane predictions in whole-genome data
-
Kall,L. and Sonnhammer,E.L. (2002) Reliability of transmembrane predictions in whole-genome data, FEBS Lett., 532, 415-418.
-
(2002)
FEBS Lett.
, vol.532
, pp. 415-418
-
-
Kall, L.1
Sonnhammer, E.L.2
-
17
-
-
0032438987
-
Hidden Markov models for detecting remote protein homologies
-
Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
18
-
-
0034717007
-
Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution
-
Kolbe,M., Besir,H., Essen,L.O. and Oesterhelt,D. (2000) Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution, Science, 288, 1390-1396.
-
(2000)
Science
, vol.288
, pp. 1390-1396
-
-
Kolbe, M.1
Besir, H.2
Essen, L.O.3
Oesterhelt, D.4
-
19
-
-
0024157070
-
Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: Symmetry relations and sequence comparisons between different species
-
Komiya,H., Yeates,T.O., Rees,D.C., Allen,J.P. and Feher,G. (1988) Structure of the reaction center from Rhodobacter sphaeroides R-26 and 2.4.1: Symmetry relations and sequence comparisons between different species. Proc. Natl Acad. Sci. USA, 85, 9012-9016.
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 9012-9016
-
-
Komiya, H.1
Yeates, T.O.2
Rees, D.C.3
Allen, J.P.4
Feher, G.5
-
20
-
-
12444274301
-
Crystal structure of the potassium channel KirBac1.1 in the closed state
-
Kuo,A., Gulbis,J.M., Antcliff,J.F., Rahman,T., Lowe,E.D., Zimmer,J., Cuthbertson,J., Ashcroft,F.M., Ezaki,T. and Doyle,D.A. (2003) Crystal structure of the potassium channel KirBac1.1 in the closed state. Science, 300, 1922-1926.
-
(2003)
Science
, vol.300
, pp. 1922-1926
-
-
Kuo, A.1
Gulbis, J.M.2
Antcliff, J.F.3
Rahman, T.4
Lowe, E.D.5
Zimmer, J.6
Cuthbertson, J.7
Ashcroft, F.M.8
Ezaki, T.9
Doyle, D.A.10
-
21
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte,J. and Doolittle,R.F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 157, 105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
22
-
-
0031854952
-
DIALIGN: Finding local similarities by multiple sequence alignment
-
Morgenstern,B., Frech,K., Dress,A. and Werner,T. (1998) DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294.
-
(1998)
Bioinformatics
, vol.14
, pp. 290-294
-
-
Morgenstern, B.1
Frech, K.2
Dress, A.3
Werner, T.4
-
23
-
-
0003939246
-
-
Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
-
Mount,D.W. (2001) Bioinformatics: Sequence and Genome Analysis, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA pp 139-204.
-
(2001)
Bioinformatics: Sequence and Genome Analysis
, pp. 139-204
-
-
Mount, D.W.1
-
24
-
-
0026673089
-
Evaluation of the predicted secondary structure of bacteriorhodopsin. Prediction of the bovine rhodopsin secondary structure and its sequence similarity with bacteriorhodopsin
-
Nero,T.L. and Louis,W.J. (1992) Evaluation of the predicted secondary structure of bacteriorhodopsin. Prediction of the bovine rhodopsin secondary structure and its sequence similarity with bacteriorhodopsin. Biochem. Int., 27, 763-770.
-
(1992)
Biochem. Int.
, vol.27
, pp. 763-770
-
-
Nero, T.L.1
Louis, W.J.2
-
25
-
-
0033670313
-
PHAT: A transmembrane-specific substitution matrix
-
Ng,P.C., Henikoff,J.G. and Henikoff,S. (2000) PHAT: A transmembrane-specific substitution matrix. Bioinformatics, 16, 760-766.
-
(2000)
Bioinformatics
, vol.16
, pp. 760-766
-
-
Ng, P.C.1
Henikoff, J.G.2
Henikoff, S.3
-
26
-
-
0036891703
-
Prediction of partial membrane protein topologies using a consensus approach
-
Nilsson,J., Persson,B. and von Heijne,G. (2002) Prediction of partial membrane protein topologies using a consensus approach. Protein Sci., 11, 2974-2980.
-
(2002)
Protein Sci.
, vol.11
, pp. 2974-2980
-
-
Nilsson, J.1
Persson, B.2
von Heijne, G.3
-
27
-
-
0027062943
-
Environment-specific amino-acid substitution tables - Tertiary templates and prediction of protein folds
-
Overington,J., Donnelly,D., Johnson,M.S., Sali,A. and Blundell,T.L. (1992) Environment-specific amino-acid substitution tables - tertiary templates and prediction of protein folds. Protein Sci., 1, 216-226.
-
(1992)
Protein Sci.
, vol.1
, pp. 216-226
-
-
Overington, J.1
Donnelly, D.2
Johnson, M.S.3
Sali, A.4
Blundell, T.L.5
-
28
-
-
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,T.I, Teller,D.C., Okada,T., Stenkamp,R.E., Yamamoto,M. and Miyano,M. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science, 289, 739-745.
-
(2000)
Science
, vol.289
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.A.6
Le, T.I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
Yamamoto, M.11
Miyano, M.12
-
29
-
-
0028279520
-
Prediction of transmembrane segments in proteins utilizing multiple sequence alignments
-
Persson,B. and Argos,P. (1994) Prediction of transmembrane segments in proteins utilizing multiple sequence alignments. J. Mol. Biol., 237, 182-192.
-
(1994)
J. Mol. Biol.
, vol.237
, pp. 182-192
-
-
Persson, B.1
Argos, P.2
-
30
-
-
0035964365
-
X-ray structure of sensory rhodopsin II at 2.1 Å resolution
-
Royant,A., Nollert,P., Edman,K., Neutze,R., Landau,E.M., Pebay-Peyroula,E. and Navarro,J. (2001) X-ray structure of sensory rhodopsin II at 2.1 Å resolution. Proc. Natl Acad. Sci USA, 98, 10131-10136.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 10131-10136
-
-
Royant, A.1
Nollert, P.2
Edman, K.3
Neutze, R.4
Landau, E.M.5
Pebay-Peyroula, E.6
Navarro, J.7
-
31
-
-
0026527758
-
Pattern-induced multi-sequence alignment (pima) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling
-
Smith,R.F. and Smith,T.F. (1992) Pattern-induced multi-sequence alignment (pima) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling. Protein Eng., 5, 35-41.
-
(1992)
Protein Eng.
, vol.5
, pp. 35-41
-
-
Smith, R.F.1
Smith, T.F.2
-
32
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
33
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
34
-
-
0026716643
-
Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule
-
von Heijne,G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 225, 487-494.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 487-494
-
-
von Heijne, G.1
|