-
1
-
-
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 Bioinf. 2006, 7:189.
-
(2006)
BMC Bioinf.
, vol.7
, pp. 189
-
-
Bagos, P.G.1
Liakopoulos, T.D.2
Hamodrakas, S.J.3
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., van Gusteren W.F., Di Nola A., Haak J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gusteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
3
-
-
35548988341
-
Common themes in the assembly and architecture of activating immune receptors
-
Call M.E., Wucherpfennig K.W. Common themes in the assembly and architecture of activating immune receptors. Nature 2007, 7:841-850.
-
(2007)
Nature
, vol.7
, pp. 841-850
-
-
Call, M.E.1
Wucherpfennig, K.W.2
-
4
-
-
0028685999
-
CART: a conserved antigen receptor transmembrane motif
-
Campbell K.S., Backstrom B.T., Tiefenthaler G., Palmer E. CART: a conserved antigen receptor transmembrane motif. Semin. Immunol. 1994, 6:393-410.
-
(1994)
Semin. Immunol.
, vol.6
, pp. 393-410
-
-
Campbell, K.S.1
Backstrom, B.T.2
Tiefenthaler, G.3
Palmer, E.4
-
5
-
-
0028103275
-
The CCP4 suite: programs for protein crystallography
-
Collaborative Computational Project Number 4
-
The CCP4 suite: programs for protein crystallography. Acta Crystallogr. Sect. D 1994, 50:760-763. Collaborative Computational Project Number 4.
-
(1994)
Acta Crystallogr. Sect. D
, vol.50
, pp. 760-763
-
-
-
6
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks G.E., Hon G., Chandonia J.M., Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 2004, 14:1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
7
-
-
33845316118
-
Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer
-
Cuthbertson J.M., Bond P.J., Sansom M.S. Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer. Biochemistry 2006, 45:14298-14310.
-
(2006)
Biochemistry
, vol.45
, pp. 14298-14310
-
-
Cuthbertson, J.M.1
Bond, P.J.2
Sansom, M.S.3
-
8
-
-
33846823909
-
Particle mesh Ewald: An N_log(N) method for Ewald sums in large systems
-
Darden T., York D., Pedersen L. Particle mesh Ewald: An N_log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98:10089-10092.
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
9
-
-
0036301006
-
Motifs of serine and threonine can drive association of transmembrane helices
-
Dawson J.P., Weinger J.S., Engelman D.M. Motifs of serine and threonine can drive association of transmembrane helices. J. Mol. Biol. 2002, 316:799-805.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 799-805
-
-
Dawson, J.P.1
Weinger, J.S.2
Engelman, D.M.3
-
11
-
-
27144505097
-
Protein identification and analysis tools on the ExPASy server
-
Humana Press, J.M. Walker (Ed.)
-
Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., Bairoch A. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook 2005, 571-607. Humana Press. J.M. Walker (Ed.).
-
(2005)
The Proteomics Protocols Handbook
, pp. 571-607
-
-
Gasteiger, E.1
Hoogland, C.2
Gattiker, A.3
Duvaud, S.4
Wilkins, M.R.5
Appel, R.D.6
Bairoch, A.7
-
12
-
-
0036135139
-
A possible role for pi-stacking in the self-assembly of amyloid fibrils
-
Gazit E. A possible role for pi-stacking in the self-assembly of amyloid fibrils. FASEB J. 2002, 16:77-83.
-
(2002)
FASEB J.
, vol.16
, pp. 77-83
-
-
Gazit, E.1
-
13
-
-
0035969998
-
Polar side chains drive the association of model transmembrane peptides
-
Gratkowski H., Lear J.D., DeGrado W.F. Polar side chains drive the association of model transmembrane peptides. Proc. Natl Acad. Sci. USA 2001, 98:880-885.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 880-885
-
-
Gratkowski, H.1
Lear, J.D.2
DeGrado, W.F.3
-
14
-
-
0242578620
-
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
-
Guindon S., Gascuel O.A. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
-
(2003)
Syst. Biol.
, vol.52
, pp. 696-704
-
-
Guindon, S.1
Gascuel, O.A.2
-
15
-
-
68149170743
-
Structural determinants of transmembrane helical proteins
-
Harrington S.E., Ben-Tal N. Structural determinants of transmembrane helical proteins. Structure 2009, 17:1092-1103.
-
(2009)
Structure
, vol.17
, pp. 1092-1103
-
-
Harrington, S.E.1
Ben-Tal, N.2
-
16
-
-
20444499328
-
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
-
Henin J., Pohorille A., Chipot C. Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A. J. Am. Chem. Soc. 2005, 127:8478-8484.
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 8478-8484
-
-
Henin, J.1
Pohorille, A.2
Chipot, C.3
-
17
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess B., Bekker H., Berendsen H.J.C., Fraaije J.G.E.M. LINCS: A linear constraint solver for molecular simulations. J. Comp. Chem. 1997, 18:1463-1472.
-
(1997)
J. Comp. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
18
-
-
0000207681
-
TMbase-A database of membrane spanning proteins segments
-
Hofmann K., Stoffel W. TMbase-A database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler 1993, 374:166.
-
(1993)
Biol. Chem. Hoppe-Seyler
, vol.374
, pp. 166
-
-
Hofmann, K.1
Stoffel, W.2
-
19
-
-
1942473116
-
Shorter side chains optimize helix-helix packing
-
Jiang S., Vakser I.A. Shorter side chains optimize helix-helix packing. Protein Sci. 2004, 13:1426-1429.
-
(2004)
Protein Sci.
, vol.13
, pp. 1426-1429
-
-
Jiang, S.1
Vakser, I.A.2
-
20
-
-
0020997912
-
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
21
-
-
0037076540
-
GXXXG and AXXXA: common alphahelical interaction motifs in proteins, particularly in extremophiles
-
Kleiger G., Grothe R., Mallick P., Eisenberg D. GXXXG and AXXXA: common alphahelical interaction motifs in proteins, particularly in extremophiles. Biochemistry 2002, 41:5990-5997.
-
(2002)
Biochemistry
, vol.41
, pp. 5990-5997
-
-
Kleiger, G.1
Grothe, R.2
Mallick, P.3
Eisenberg, D.4
-
22
-
-
17744396121
-
Not so different after all: a comparison of methods for detecting amino acid sites under selection
-
Kosakovsky Pond S.L., Frost S.D. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 2005, 22:1208-1222.
-
(2005)
Mol. Biol. Evol.
, vol.22
, pp. 1208-1222
-
-
Kosakovsky Pond, S.L.1
Frost, S.D.2
-
23
-
-
36448991500
-
ClustalW and ClustalX version 2
-
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. ClustalW and ClustalX version 2. Bioinformatics 2007, 23(21):2947-2948.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
24
-
-
0000243829
-
PROCHECK: a program to check the stereochemical quality of protein structures
-
Laskowski R.A., MacArthur M.W., Moss M.D., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993, 26:283-291.
-
(1993)
J. Appl. Cryst.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, M.D.3
Thornton, J.M.4
-
25
-
-
0027772959
-
Shape complementarity at protein/protein interfaces
-
Lawrence M.C., Colman P.M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 1993, 234:946-950.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 946-950
-
-
Lawrence, M.C.1
Colman, P.M.2
-
26
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le S.Q., Gascuel O. An improved general amino acid replacement matrix. Mol. Biol. Evol. 2008, 25:1307-1320.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
27
-
-
0026686793
-
Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices
-
Lemmon M.A., Flanagan J.M., Hunt J.F., Adair B.D., Bormann B.J., Dempsey C.E., Engelman D.M. Glycophorin A dimerization is driven by specific interactions between transmembrane alpha-helices. J. Biol. Chem. 1992, 267:7683-7689.
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 7683-7689
-
-
Lemmon, M.A.1
Flanagan, J.M.2
Hunt, J.F.3
Adair, B.D.4
Bormann, B.J.5
Dempsey, C.E.6
Engelman, D.M.7
-
28
-
-
0030932407
-
A transmembrane helix dimer: structure and implications
-
MacKenzie K.R., Prestegard J.H., Engelman D.M. A transmembrane helix dimer: structure and implications. Science 1997, 276:131-133.
-
(1997)
Science
, vol.276
, pp. 131-133
-
-
MacKenzie, K.R.1
Prestegard, J.H.2
Engelman, D.M.3
-
29
-
-
0032546782
-
Pi-Stacking interactions. Alive and well in proteins
-
McGaughey G.B., Gagné M., Rappé A.K. Pi-Stacking interactions. Alive and well in proteins. J. Biol. Chem. 1998, 273:15458-15463.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 15458-15463
-
-
McGaughey, G.B.1
Gagné, M.2
Rappé, A.K.3
-
30
-
-
24044506284
-
The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase
-
Merlino A., Mazzarella L., Di Fiore A., Carannante A., Notomista E., Di Donato A., Sica F. The importance of dynamic effects on the enzyme activity: X-ray structure and molecular dynamics of onconase. J. Biol. Chem. 2005, 280:17953-17960.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 17953-17960
-
-
Merlino, A.1
Mazzarella, L.2
Di Fiore, A.3
Carannante, A.4
Notomista, E.5
Di Donato, A.6
Sica, F.7
-
31
-
-
33646794342
-
Polyglutamine repeats and beta-helix structure: molecular dynamics study
-
Merlino A., Esposito L., Vitagliano L. Polyglutamine repeats and beta-helix structure: molecular dynamics study. Proteins 2006, 63:918-927.
-
(2006)
Proteins
, vol.63
, pp. 918-927
-
-
Merlino, A.1
Esposito, L.2
Vitagliano, L.3
-
32
-
-
53649088129
-
Structure and dimerization of the teleost transmembrane immunoglobulin region
-
Merlino A., Variale S., Coscia M.R., Mazzarella L., Oreste U. Structure and dimerization of the teleost transmembrane immunoglobulin region. J. Mol. Graph. Model. 2008, 27:401-407.
-
(2008)
J. Mol. Graph. Model.
, vol.27
, pp. 401-407
-
-
Merlino, A.1
Variale, S.2
Coscia, M.R.3
Mazzarella, L.4
Oreste, U.5
-
33
-
-
33644844890
-
Energetics of the native and non-native states of the glycophorin transmembrane helix dimer
-
Mottamal M., Zhang J., Lazaridis T. Energetics of the native and non-native states of the glycophorin transmembrane helix dimer. Proteins 2006, 62:996-1009.
-
(2006)
Proteins
, vol.62
, pp. 996-1009
-
-
Mottamal, M.1
Zhang, J.2
Lazaridis, T.3
-
34
-
-
0343081370
-
X-Ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles
-
Okada T., Le Trong I., Fox B.A., Behnke C.A., Stenkamp R.E., Palczewski K. X-Ray diffraction analysis of three-dimensional crystals of bovine rhodopsin obtained from mixed micelles. J. Struct. Biol. 2000, 130:73-80.
-
(2000)
J. Struct. Biol.
, vol.130
, pp. 73-80
-
-
Okada, T.1
Le Trong, I.2
Fox, B.A.3
Behnke, C.A.4
Stenkamp, R.E.5
Palczewski, K.6
-
35
-
-
21544476177
-
Variable lymphocyte receptors in hagfish
-
Pancer Z., Saha N.R., Kasamatsu J., Suzuki T., Amemiya C.T., Kasahara M., Cooper M.D. Variable lymphocyte receptors in hagfish. Proc. Natl Acad. Sci. USA 2005, 102:9224-9229.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 9224-9229
-
-
Pancer, Z.1
Saha, N.R.2
Kasamatsu, J.3
Suzuki, T.4
Amemiya, C.T.5
Kasahara, M.6
Cooper, M.D.7
-
36
-
-
14844343601
-
Changes in interhelical hydrogen bonding upon rhodopsin activation
-
Patel A.B., Crocker E., Reeves P.J., Getmanova E.V., Eilers M., Khorana H.G., Smith S.O. Changes in interhelical hydrogen bonding upon rhodopsin activation. J. Mol. Biol. 2005, 347:803-812.
-
(2005)
J. Mol. Biol.
, vol.347
, pp. 803-812
-
-
Patel, A.B.1
Crocker, E.2
Reeves, P.J.3
Getmanova, E.V.4
Eilers, M.5
Khorana, H.G.6
Smith, S.O.7
-
37
-
-
66149134063
-
Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs
-
Prilusky J., Eitan B. Studying membrane proteins through the eyes of the genetic code revealed a strong uracil bias in their coding mRNAs. Proc. Natl Acad. Sci. USA 2009, 106:6662-6666.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 6662-6666
-
-
Prilusky, J.1
Eitan, B.2
-
38
-
-
3142702159
-
Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish
-
Rumfelt L.L., Diaz M., Lohr R.L., Mochon E., Flajnik M.F. Unprecedented multiplicity of Ig transmembrane and secretory mRNA forms in the cartilaginous fish. J. Immunol. 2004, 173:1129-1139.
-
(2004)
J. Immunol.
, vol.173
, pp. 1129-1139
-
-
Rumfelt, L.L.1
Diaz, M.2
Lohr, R.L.3
Mochon, E.4
Flajnik, M.F.5
-
39
-
-
5144227144
-
Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions
-
Schneider D., Engelman D.M. Motifs of two small residues can assist but are not sufficient to mediate transmembrane helix interactions. J. Mol. Biol. 2004, 343:799-804.
-
(2004)
J. Mol. Biol.
, vol.343
, pp. 799-804
-
-
Schneider, D.1
Engelman, D.M.2
-
40
-
-
0025008168
-
Sequence logos: a new way to display consensus sequences
-
Schneider T.D., Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990, 18:6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.M.2
-
41
-
-
0034711958
-
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions
-
Senes A., Gerstein M., Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. J. Mol. Biol. 2000, 296:921-936.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 921-936
-
-
Senes, A.1
Gerstein, M.2
Engelman, D.M.3
-
42
-
-
0031427052
-
Entropy analysis of immunoglobulin and T cell receptor
-
Stewart J.J., Lee C.Y., Ibrahim S., Watts P., Shlomchik M., Weigert M., Litwin S. Entropy analysis of immunoglobulin and T cell receptor. Mol. Immunol. 1997, 34:1067-1082.
-
(1997)
Mol. Immunol.
, vol.34
, pp. 1067-1082
-
-
Stewart, J.J.1
Lee, C.Y.2
Ibrahim, S.3
Watts, P.4
Shlomchik, M.5
Weigert, M.6
Litwin, S.7
-
43
-
-
0031574072
-
The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools
-
Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface. Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 4876-4882
-
-
Thompson, J.D.1
Gibson, T.J.2
Plewniak, F.3
Jeanmougin, F.4
Higgins, D.G.5
-
44
-
-
11244328066
-
Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers
-
Vaccaro L., Cross K.J., Kleinjung J., Straus S.K., Thomas D.J., Wharton S.A., Skehel J.J., Fraternali F. Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers. Biophys. J. 2005, 88:25-36.
-
(2005)
Biophys. J.
, vol.88
, pp. 25-36
-
-
Vaccaro, L.1
Cross, K.J.2
Kleinjung, J.3
Straus, S.K.4
Thomas, D.J.5
Wharton, S.A.6
Skehel, J.J.7
Fraternali, F.8
-
45
-
-
34548757937
-
Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study
-
Vereshaga Y.A., Volynsky P.E., Pustovalova J.E., Nolde D.E., Arseniev A.S., Efremov R.G. Specificity of helix packing in transmembrane dimer of the cell death factor BNIP3: a molecular modeling study. Proteins 2007, 69:309-325.
-
(2007)
Proteins
, vol.69
, pp. 309-325
-
-
Vereshaga, Y.A.1
Volynsky, P.E.2
Pustovalova, J.E.3
Nolde, D.E.4
Arseniev, A.S.5
Efremov, R.G.6
-
47
-
-
0007949690
-
Interhelical hydrogen bonding drives strong interactions in membrane proteins
-
Zhou F.X., Cocco M.J., Russ W.P., Brunger A.T., Engelman D.M. Interhelical hydrogen bonding drives strong interactions in membrane proteins. Nat. Struct. Biol. 2000, 7:154-160.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 154-160
-
-
Zhou, F.X.1
Cocco, M.J.2
Russ, W.P.3
Brunger, A.T.4
Engelman, D.M.5
|