-
1
-
-
34547622288
-
Modeling charged protein side chains in lipid membranes
-
Allen T.W. Modeling charged protein side chains in lipid membranes. J. Gen. Physiol. 130 (2007) 237-240
-
(2007)
J. Gen. Physiol.
, vol.130
, pp. 237-240
-
-
Allen, T.W.1
-
2
-
-
45149114391
-
Reconstruction of protein backbones from the brix collection of canonical protein fragments
-
Baeten L., Reumers J., Tur V., Stricher F., Lenaerts T., Serrano L., Rousseau F., and Schymkowitz J. Reconstruction of protein backbones from the brix collection of canonical protein fragments. PLoS Comput. Biol. 4 (2008) e1000083
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Baeten, L.1
Reumers, J.2
Tur, V.3
Stricher, F.4
Lenaerts, T.5
Serrano, L.6
Rousseau, F.7
Schymkowitz, J.8
-
4
-
-
0033994775
-
Helanal: a program to characterize helix geometry in proteins
-
Bansal M., Kumar S., and Velavan R. Helanal: a program to characterize helix geometry in proteins. J. Biomol. Struct. Dyn. 17 (2000) 811-819
-
(2000)
J. Biomol. Struct. Dyn.
, vol.17
, pp. 811-819
-
-
Bansal, M.1
Kumar, S.2
Velavan, R.3
-
5
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 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
-
6
-
-
28444488355
-
Solving the membrane protein folding problem
-
Bowie J.U. Solving the membrane protein folding problem. Nature 438 (2005) 581-589
-
(2005)
Nature
, vol.438
, pp. 581-589
-
-
Bowie, J.U.1
-
7
-
-
34247186195
-
-
University of California, San Francisco
-
Case D.A., Darden T.A., Cheatham III T.E., Simmerling C.L., Wang J., Duke R.E., Luo R., Merz K.M., Pearlman D.A., Crowley M., Walker R.C., Zhang W., Wang B., Hayik S., Roitberg A., Seabra G., Wong K.F., Paesani F., Wu X., Brozell S., Tsui V., Gohlke H., Yang L., Tan C., Mongan J., Hornak V., Cui G., Beroza P., Mathews D.H., Schafmeister C., Ross W.S., and Kollman P.A. AMBER 9 (2006), University of California, San Francisco
-
(2006)
AMBER 9
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Pearlman, D.A.9
Crowley, M.10
Walker, R.C.11
Zhang, W.12
Wang, B.13
Hayik, S.14
Roitberg, A.15
Seabra, G.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.20
Tsui, V.21
Gohlke, H.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Beroza, P.28
Mathews, D.H.29
Schafmeister, C.30
Ross, W.S.31
Kollman, P.A.32
more..
-
8
-
-
16344378642
-
Analysis of side-chain rotamers in transmembrane proteins
-
Chamberlain A.K., and Bowie J.U. Analysis of side-chain rotamers in transmembrane proteins. Biophys. J. 87 (2004) 3460-3469
-
(2004)
Biophys. J.
, vol.87
, pp. 3460-3469
-
-
Chamberlain, A.K.1
Bowie, J.U.2
-
9
-
-
0021422888
-
Energetic approach to the packing of α-helices. 2. General treatment of nonequivalent and nonregular helices
-
Chou K.C., Nemethy G., and Scheraga H.A. Energetic approach to the packing of α-helices. 2. General treatment of nonequivalent and nonregular helices. J. Am. Chem. Soc. 106 (1984) 3161-3170
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 3161-3170
-
-
Chou, K.C.1
Nemethy, G.2
Scheraga, H.A.3
-
10
-
-
0036430199
-
Proline-induced distortions of transmembrane helices
-
Cordes F.S., Bright J.N., and Sansom M.S. Proline-induced distortions of transmembrane helices. J. Mol. Biol. 323 (2002) 951-960
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 951-960
-
-
Cordes, F.S.1
Bright, J.N.2
Sansom, M.S.3
-
11
-
-
0036301006
-
Motifs of serine and threonine can drive association of transmembrane helices
-
Dawson J.P., Weinger J.S., and Engelman D.M. Motifs of serine and threonine can drive association of transmembrane helices. J. Mol. Biol. 316 (2002) 799-805
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 799-805
-
-
Dawson, J.P.1
Weinger, J.S.2
Engelman, D.M.3
-
12
-
-
0347949636
-
Ser and thr residues modulate the conformation of pro-kinked transmembrane alpha-helices
-
Deupi X., Olivella M., Govaerts C., Ballesteros J.A., Campillo M., and Pardo L. Ser and thr residues modulate the conformation of pro-kinked transmembrane alpha-helices. Biophys. J. 86 (2004) 105-115
-
(2004)
Biophys. J.
, vol.86
, pp. 105-115
-
-
Deupi, X.1
Olivella, M.2
Govaerts, C.3
Ballesteros, J.A.4
Campillo, M.5
Pardo, L.6
-
13
-
-
34447258678
-
Structural models of class a G protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity
-
Deupi X., Dolker N., Lopez-Rodriguez M., Campillo M., Ballesteros J., and Pardo L. Structural models of class a G protein-coupled receptors as a tool for drug design: insights on transmembrane bundle plasticity. Curr. Top. Med. Chem. 7 (2007) 999-1006
-
(2007)
Curr. Top. Med. Chem.
, vol.7
, pp. 999-1006
-
-
Deupi, X.1
Dolker, N.2
Lopez-Rodriguez, M.3
Campillo, M.4
Ballesteros, J.5
Pardo, L.6
-
14
-
-
0036226583
-
Comparison of helix interactions in membrane and soluble alpha-bundle proteins
-
Eilers M., Patel A.B., Liu W., and Smith S.O. Comparison of helix interactions in membrane and soluble alpha-bundle proteins. Biophys. J. 82 (2002) 2720-2736
-
(2002)
Biophys. J.
, vol.82
, pp. 2720-2736
-
-
Eilers, M.1
Patel, A.B.2
Liu, W.3
Smith, S.O.4
-
17
-
-
72449206137
-
-
Frisch, M.J, Trucks, G.W, Schlegel, H.B, Scuseria, G.E, Robb, M.A, Cheeseman, J.R, Montgomery, J.J.A, Vreven, T, Kudin, K.N, Burant, J.C, Millam, J.M, Iyengar, S.S, Tomasi, J, Barone, V, Mennucci, B, Cossi, M, Scalmani, G, Rega, N, Petersson, G.A, Nakatsuji, H, Hada, M, Ehara, M, Toyota, K, Fukuda, R, Hasegawa, J, Ishida, M, Nakajima, T, Honda, Y, Kitao, O, Nakai, H, Klene, M, Li, X, Knox, J.E, Hratchian, H.P, Cross, J.B, Bakken, V, Adamo, C, Jaramillo, J, Gomperts, R, Stratmann, R.E, Yazyev, O, Austin, A.J, Cammi, R, Pomelli, C, Ochterski, J.W, Ayala, P.Y, Morokuma, K, Voth, G.A, Salvador, P, Dannenberg, J.J, Zakrzewski, V.G, Dapprich, S, Daniels, A.D, Strain, M.C, Farkas, O, Malick, D.K, Rabuck, A.D, Raghavachari, K, Foresman, J.B, Ortiz, J.V, Cui, Q, Baboul, A.G, Clifford, S, Cioslowski, J, Stefanov, B.B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Martin, R.L, Fox, D.J, Keith, T, Laham, M.A.A, Peng, C.Y, N
-
Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Montgomery, J.J.A., Vreven, T., Kudin, K.N., Burant, J.C., Millam, J.M., Iyengar, S.S., Tomasi, J., Barone, V., Mennucci, B., Cossi, M., Scalmani, G., Rega, N., Petersson, G.A., Nakatsuji, H., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Klene, M., Li, X., Knox, J.E., Hratchian, H.P., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Ayala, P.Y., Morokuma, K., Voth, G.A., Salvador, P., Dannenberg, J.J., Zakrzewski, V.G., Dapprich, S., Daniels, A.D., Strain, M.C., Farkas, O., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Ortiz, J.V., Cui, Q., Baboul, A.G., Clifford, S., Cioslowski, J., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Martin, R.L., Fox, D.J., Keith, T., Laham, M.A.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Gonzalez, C., Pople, J.A., 2004. Gaussian 03, Revision d.01.
-
-
-
-
18
-
-
0035918313
-
The TxP motif in the second transmembrane helix of CCR5: a structural determinant in chemokine-induced activation
-
Govaerts C., Blanpain C., Deupi X., Ballet S., Ballesteros J.A., Wodak S.J., Vassart G., Pardo L., and Parmentier M. The TxP motif in the second transmembrane helix of CCR5: a structural determinant in chemokine-induced activation. J. Biol. Chem. 276 (2001) 13217-13225
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 13217-13225
-
-
Govaerts, C.1
Blanpain, C.2
Deupi, X.3
Ballet, S.4
Ballesteros, J.A.5
Wodak, S.J.6
Vassart, G.7
Pardo, L.8
Parmentier, M.9
-
19
-
-
0021755525
-
Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins
-
Gray T.M., and Matthews B.W. Intrahelical hydrogen bonding of serine, threonine and cysteine residues within alpha-helices and its relevance to membrane-bound proteins. J. Mol. Biol. 175 (1984) 75-81
-
(1984)
J. Mol. Biol.
, vol.175
, pp. 75-81
-
-
Gray, T.M.1
Matthews, B.W.2
-
20
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., and Simmerling C. Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65 (2006) 712-725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
21
-
-
0004014257
-
-
Department of Biochemistry and Molecular Biology, University College, London
-
Hubbart S.J., and Thornton J.M. NACCESS (1993), Department of Biochemistry and Molecular Biology, University College, London
-
(1993)
NACCESS
-
-
Hubbart, S.J.1
Thornton, J.M.2
-
22
-
-
46249089993
-
Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins
-
Joh N.H., Min A., Faham S., Whitelegge J.P., Yang D., Woods V.L., and Bowie J.U. Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins. Nature 453 (2008) 1266-1270
-
(2008)
Nature
, vol.453
, pp. 1266-1270
-
-
Joh, N.H.1
Min, A.2
Faham, S.3
Whitelegge, J.P.4
Yang, D.5
Woods, V.L.6
Bowie, J.U.7
-
24
-
-
0029831680
-
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally-related subfamilies
-
Kelley L.A., Gardner S.P., and Sutcliffe M.J. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally-related subfamilies. Protein Eng. 9 (1996) 1063-1065
-
(1996)
Protein Eng.
, vol.9
, pp. 1063-1065
-
-
Kelley, L.A.1
Gardner, S.P.2
Sutcliffe, M.J.3
-
26
-
-
0036084957
-
Design, synthesis and pharmacological evaluation of 5-hydroxytryptamine(1a) receptor ligands to explore the three-dimensional structure of the receptor
-
Lopez-Rodriguez M.L., Vicente B., Deupi X., Barrondo S., Olivella M., Morcillo M.J., Behamu B., Ballesteros J.A., Salles J., and Pardo L. Design, synthesis and pharmacological evaluation of 5-hydroxytryptamine(1a) receptor ligands to explore the three-dimensional structure of the receptor. Mol. Pharmacol. 62 (2002) 15-21
-
(2002)
Mol. Pharmacol.
, vol.62
, pp. 15-21
-
-
Lopez-Rodriguez, M.L.1
Vicente, B.2
Deupi, X.3
Barrondo, S.4
Olivella, M.5
Morcillo, M.J.6
Behamu, B.7
Ballesteros, J.A.8
Salles, J.9
Pardo, L.10
-
27
-
-
0023521842
-
Analysis of the relationship between side-chain conformation and secondary structure in globular proteins
-
McGregor M.J., Islam S.A., and Sternberg M.J.E. Analysis of the relationship between side-chain conformation and secondary structure in globular proteins. J. Mol. Biol. 198 (1987) 295-310
-
(1987)
J. Mol. Biol.
, vol.198
, pp. 295-310
-
-
McGregor, M.J.1
Islam, S.A.2
Sternberg, M.J.E.3
-
28
-
-
0033597281
-
A turn propensity scale for transmembrane helices
-
Monne M., Hermansson M., and von Heijne G. A turn propensity scale for transmembrane helices. J. Mol. Biol. 288 (1999) 141-145
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 141-145
-
-
Monne, M.1
Hermansson, M.2
von Heijne, G.3
-
29
-
-
0345701501
-
Highly conserved serine in the third transmembrane helix of the luteinizing hormone/human chorionic gonadotropin receptor regulates receptor activation
-
Munshi U.M., Pogozheva I.D., and Menon K.M. Highly conserved serine in the third transmembrane helix of the luteinizing hormone/human chorionic gonadotropin receptor regulates receptor activation. Biochemistry 42 (2003) 3708-3715
-
(2003)
Biochemistry
, vol.42
, pp. 3708-3715
-
-
Munshi, U.M.1
Pogozheva, I.D.2
Menon, K.M.3
-
30
-
-
65449161390
-
Ligand binding and micro-switches in 7tm receptor structures
-
Nygaard R., Frimurer T.M., Holst B., Rosenkilde M.M., and Schwartz T.W. Ligand binding and micro-switches in 7tm receptor structures. Trends Pharmacol. Sci. 30 (2009) 249-259
-
(2009)
Trends Pharmacol. Sci.
, vol.30
, pp. 249-259
-
-
Nygaard, R.1
Frimurer, T.M.2
Holst, B.3
Rosenkilde, M.M.4
Schwartz, T.W.5
-
31
-
-
0036104783
-
Influence of the environment in the conformation of alpha-helices studied by protein database search and molecular dynamics simulations
-
Olivella M., Deupi X., Govaerts C., and Pardo L. Influence of the environment in the conformation of alpha-helices studied by protein database search and molecular dynamics simulations. Biophys. J. 82 (2002) 3207-3213
-
(2002)
Biophys. J.
, vol.82
, pp. 3207-3213
-
-
Olivella, M.1
Deupi, X.2
Govaerts, C.3
Pardo, L.4
-
32
-
-
1542376209
-
Missense mutations in transmembrane domains of proteins: phenotypic propensity of polar residues for human disease
-
Partridge A.W., Therien A.G., and Deber C.M. Missense mutations in transmembrane domains of proteins: phenotypic propensity of polar residues for human disease. Proteins 54 (2004) 648-656
-
(2004)
Proteins
, vol.54
, pp. 648-656
-
-
Partridge, A.W.1
Therien, A.G.2
Deber, C.M.3
-
33
-
-
63849323943
-
4 receptors
-
4 receptors. Mol. Pharmacol. 75 (2009) 982-990
-
(2009)
Mol. Pharmacol.
, vol.75
, pp. 982-990
-
-
Pellissier, L.1
Sallander, J.2
Campillo, M.3
Gaven, F.4
Queffeulou, E.5
Pillot, M.6
Dumuis, A.7
Claeysen, S.8
Bockaert, J.9
Pardo, L.10
-
34
-
-
0035895421
-
Non-alpha-helical elements modulate polytopic membrane protein architecture
-
Riek R.P., Rigoutsos I., Novotny J., and Graham R.M. Non-alpha-helical elements modulate polytopic membrane protein architecture. J. Mol. Biol. 306 (2001) 349-362
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 349-362
-
-
Riek, R.P.1
Rigoutsos, I.2
Novotny, J.3
Graham, R.M.4
-
35
-
-
0041660896
-
Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors
-
Rigoutsos I., Riek P., Graham R.M., and Novotny J. Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. Nucleic Acids Res. 31 (2003) 4625-4631
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4625-4631
-
-
Rigoutsos, I.1
Riek, P.2
Graham, R.M.3
Novotny, J.4
-
36
-
-
66249144426
-
The structure and function of g-protein-coupled receptors
-
Rosenbaum D.M., Rasmussen S.G., and Kobilka B.K. The structure and function of g-protein-coupled receptors. Nature 459 (2009) 356-363
-
(2009)
Nature
, vol.459
, pp. 356-363
-
-
Rosenbaum, D.M.1
Rasmussen, S.G.2
Kobilka, B.K.3
-
37
-
-
0034327611
-
Hinges, swivels and switches: the role of prolines in signalling via transmembrane α-helices
-
Sansom M.S.P., and Weinstein H. Hinges, swivels and switches: the role of prolines in signalling via transmembrane α-helices. Trends Pharmacol. Sci. 21 (2000) 445-451
-
(2000)
Trends Pharmacol. Sci.
, vol.21
, pp. 445-451
-
-
Sansom, M.S.P.1
Weinstein, H.2
-
38
-
-
0034711958
-
Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with β-branched residues at neighboring positions
-
Senes A., Gerstein M., and Engelman D.M. Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with β-branched residues at neighboring positions. J. Mol. Biol. 296 (2000) 921-936
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 921-936
-
-
Senes, A.1
Gerstein, M.2
Engelman, D.M.3
-
39
-
-
33847081648
-
Pharmacogenomic and structural analysis of constitutive g protein-coupled receptor activity
-
Smit M.J., Vischer H.F., Bakker R.A., Jongejan A., Timmerman H., Pardo L., and Leurs R. Pharmacogenomic and structural analysis of constitutive g protein-coupled receptor activity. Annu. Rev. Pharmacol. Toxicol. 47 (2007) 53-87
-
(2007)
Annu. Rev. Pharmacol. Toxicol.
, vol.47
, pp. 53-87
-
-
Smit, M.J.1
Vischer, H.F.2
Bakker, R.A.3
Jongejan, A.4
Timmerman, H.5
Pardo, L.6
Leurs, R.7
-
40
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, rna, and phosphoramidate - DNA helices
-
Srinivasan J., Cheatham T.E., Cieplak P., Kollman P.A., and Case D.A. Continuum solvent studies of the stability of DNA, rna, and phosphoramidate - DNA helices. J. Am. Chem. Soc. 120 (1998) 9401-9409
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
41
-
-
84961980477
-
Quantum mechanical continuum solvation models
-
Tomasi J., Mennucci B., and Cammi R. Quantum mechanical continuum solvation models. Chem. Rev. 105 (2005) 2999-3093
-
(2005)
Chem. Rev.
, vol.105
, pp. 2999-3093
-
-
Tomasi, J.1
Mennucci, B.2
Cammi, R.3
-
42
-
-
13444280419
-
PDM_TM: selection and membrane localization of transmembrane proteins in the protein data bank
-
Tusnady G.E., Dosztanyi Z., and Simon I. PDM_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33 (2005) D275-D278
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Tusnady, G.E.1
Dosztanyi, Z.2
Simon, I.3
-
43
-
-
0742288411
-
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
-
Yohannan S., Faham S., Yang D., Whitelegge J.P., and Bowie J.U. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. USA 101 (2004) 959-963
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 959-963
-
-
Yohannan, S.1
Faham, S.2
Yang, D.3
Whitelegge, J.P.4
Bowie, J.U.5
|