-
1
-
-
0032987478
-
Membrane protein folding and stability: Physical principles
-
White SH, Wimley WC (1999) Membrane protein folding and stability: physical principles. Annu Rev Bioph Biomol Struct 28:319-365
-
(1999)
Annu Rev Bioph Biomol Struct
, vol.28
, pp. 319-365
-
-
White, S.H.1
Wimley, W.C.2
-
2
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J (2000) Drug discovery: a historical perspective. Science 287(5460):1960-1964
-
(2000)
Science
, vol.287
, Issue.5460
, pp. 1960-1964
-
-
Drews, J.1
-
3
-
-
33845890639
-
It's a GPCR world
-
Filmore D (2004) It's a GPCR world. Mod Drug Discov 7:24-26
-
(2004)
Mod Drug Discov
, vol.7
, pp. 24-26
-
-
Filmore, D.1
-
4
-
-
28444488355
-
Solving the membrane protein folding problem
-
doi:10.1038/nature04395
-
Bowie JU (2005) Solving the membrane protein folding problem. Nature 438(7068):581-589. doi:10.1038/nature04395
-
(2005)
Nature
, vol.438
, Issue.7068
, pp. 581-589
-
-
Bowie, J.U.1
-
5
-
-
0026661869
-
Spontaneous insertion of polypeptidechains into membranes - A Monte-Carlo model
-
Milik M, Skolnick J (1992) Spontaneous insertion of polypeptidechains into membranes - a Monte-Carlo model. Proc Natl Acad Sci USA 89(20):9391-9395
-
(1992)
Proc Natl Acad Sci USA
, vol.89
, Issue.20
, pp. 9391-9395
-
-
Milik, M.1
Skolnick, J.2
-
6
-
-
4243379922
-
Lattice model of transmembrane polypeptide folding
-
Chen CM (2001) Lattice model of transmembrane polypeptide folding. Phys Rev E 63(1):010901
-
(2001)
Phys Rev e
, vol.63
, Issue.1
, pp. 010901
-
-
Chen, C.M.1
-
7
-
-
0034718560
-
Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor
-
Floriano WB, Vaidehi N, Goddard WA, Singer MS, Shepherd GM (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci USA 97(20):10712-10716
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, Issue.20
, pp. 10712-10716
-
-
Floriano, W.B.1
Vaidehi, N.2
Goddard, W.A.3
Singer, M.S.4
Shepherd, G.M.5
-
8
-
-
0037110551
-
Optimal potentials for predicting inter-helical packing in transmembrane proteins
-
doi:10.1002/prot.10229
-
Dobbs H, Orlandini E, Bonaccini R, Seno F (2002) Optimal potentials for predicting inter-helical packing in transmembrane proteins. Proteins 49(3):342-349. doi:10.1002/prot.10229
-
(2002)
Proteins
, vol.49
, Issue.3
, pp. 342-349
-
-
Dobbs, H.1
Orlandini, E.2
Bonaccini, R.3
Seno, F.4
-
9
-
-
0037339560
-
Computer Simulations of membrane protein folding: Structure and dynamics
-
Chen CM, Chen CC (2003) Computer Simulations of membrane protein folding: structure and dynamics. Biophys J 84(3):1902- 1908
-
(2003)
Biophys J
, vol.84
, Issue.3
, pp. 1902-1908
-
-
Chen, C.M.1
Chen, C.C.2
-
10
-
-
2942639959
-
Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation
-
-):. doi:10.1016/j. cplett.2004.04.112
-
Kokubo H, Okamoto Y (2004) Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation. Chem Phys Lett 392(1-3):168-175. doi:10.1016/j. cplett.2004.04.112
-
(2004)
Chem Phys Lett
, vol.392
, Issue.1-3
, pp. 168-175
-
-
Kokubo, H.1
Okamoto, Y.2
-
11
-
-
57149146836
-
A dual-scale approach toward structure prediction of retinal proteins
-
doi:10.1016/j.jsb.2008.10.001
-
Chen CC, Chen CM (2009) A dual-scale approach toward structure prediction of retinal proteins. J Struct Biol 165(1): 37-46. doi:10.1016/j.jsb.2008.10.001
-
(2009)
J Struct Biol
, vol.165
, Issue.1
, pp. 37-46
-
-
Chen, C.C.1
Chen, C.M.2
-
12
-
-
42649115134
-
Packing of transmembrane helices in bacteriorhodopsin folding: Structure and thermodynamics
-
doi:10.1016/ j.jsb.2008.01.003
-
Chen CC, Wei CC, Sun YC, Chen CM (2008) Packing of transmembrane helices in bacteriorhodopsin folding: structure and thermodynamics. J Struct Biol 162(2):237-247. doi:10.1016/ j.jsb.2008.01.003
-
(2008)
J Struct Biol
, vol.162
, Issue.2
, pp. 237-247
-
-
Chen, C.C.1
Wei, C.C.2
Sun, Y.C.3
Chen, C.M.4
-
13
-
-
0024290472
-
Amino acid preferences for specific locations at the ends of alpha helices
-
Richardson JS, Richardson DC (1988) Amino acid preferences for specific locations at the ends of alpha helices. Science 240(4859):1648-1652
-
(1988)
Science
, vol.240
, Issue.4859
, pp. 1648-1652
-
-
Richardson, J.S.1
Richardson, D.C.2
-
14
-
-
0346996695
-
Influence of proline residues in transmembrane helix packing
-
Orzaez M, Salgado J, Gimenez-Giner A, Perez-Paya E, Mingarro I (2004) Influence of proline residues in transmembrane helix packing. J Mol Biol 335(2):631-640
-
(2004)
J Mol Biol
, vol.335
, Issue.2
, pp. 631-640
-
-
Orzaez, M.1
Salgado, J.2
Gimenez-Giner, A.3
Perez-Paya, E.4
Mingarro, I.5
-
15
-
-
1842866228
-
Proline residues in transmembrane segment IV are critical for activity, expression and targeting of the Na+/H+ exchanger isoform 1
-
Pt ):. doi:10.1042/BJ20030884
-
Slepkov ER, Chow S, Lemieux MJ, Fliegel L (2004) Proline residues in transmembrane segment IV are critical for activity, expression and targeting of the Na+/H+ exchanger isoform 1. Biochem J 379(Pt 1):31-38. doi:10.1042/ BJ20030884
-
(2004)
Biochem J
, vol.379
, Issue.1
, pp. 31-38
-
-
Slepkov, E.R.1
Chow, S.2
Lemieux, M.J.3
Fliegel, L.4
-
16
-
-
0036343993
-
Conformational dynamics of helix S6 from Shaker potassium channel: Simulation studies
-
doi:10.1002/ bip.10197
-
Bright JN, Shrivastava IH, Cordes FS, Sansom MS (2002) Conformational dynamics of helix S6 from Shaker potassium channel: simulation studies. Biopolymers 64(6):303-313. doi:10.1002/ bip.10197
-
(2002)
Biopolymers
, vol.64
, Issue.6
, pp. 303-313
-
-
Bright, J.N.1
Shrivastava, I.H.2
Cordes, F.S.3
Sansom, M.S.4
-
18
-
-
33344465109
-
Amino acid propensities for secondary structures are influenced by the protein structural class
-
doi:10.1016/j.bbrc.2006.01.159
-
Costantini S, Colonna G, Facchiano AM (2006) Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun 342(2):441-451. doi:10.1016/j.bbrc.2006.01.159
-
(2006)
Biochem Biophys Res Commun
, vol.342
, Issue.2
, pp. 441-451
-
-
Costantini, S.1
Colonna, G.2
Facchiano, A.M.3
-
19
-
-
0035895421
-
Non-alphahelical elements modulate polytopic membrane protein architecture
-
doi:10.1006/jmbi.2000.4402
-
Riek RP, Rigoutsos I, Novotny J, Graham RM (2001) Non-alphahelical elements modulate polytopic membrane protein architecture. J Mol Biol 306(2):349-362. doi:10.1006/jmbi.2000.4402
-
(2001)
J Mol Biol
, vol.306
, Issue.2
, pp. 349-362
-
-
Riek, R.P.1
Rigoutsos, I.2
Novotny, J.3
Graham, R.M.4
-
20
-
-
67349266230
-
Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction
-
doi:10.1016/j.jmgm.2009.02.004
-
Hall SE, Roberts K, Vaidehi N (2009) Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction. J Mol Graph Model 27(8):944-950. doi:10.1016/j.jmgm.2009.02.004
-
(2009)
J Mol Graph Model
, vol.27
, Issue.8
, pp. 944-950
-
-
Hall, S.E.1
Roberts, K.2
Vaidehi, N.3
-
21
-
-
0742288411
-
The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
-
doi:10.1073/pnas.0306077101
-
Yohannan S, Faham S, Yang D, Whitelegge JP, Bowie JU (2004) The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc Natl Acad Sci USA 101(4):959-963. doi:10.1073/pnas.0306077101
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, Issue.4
, pp. 959-963
-
-
Yohannan, S.1
Faham, S.2
Yang, D.3
Whitelegge, J.P.4
Bowie, J.U.5
-
22
-
-
84861434240
-
Shifting hydrogen bonds may produce flexible transmembrane helices
-
doi:10.1073/pnas.1201298109
-
Cao Z, Bowie JU (2012) Shifting hydrogen bonds may produce flexible transmembrane helices. Proc Natl Acad Sci USA 109(21):8121-8126. doi:10.1073/pnas.1201298109
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.21
, pp. 8121-8126
-
-
Cao, Z.1
Bowie, J.U.2
-
23
-
-
78650702465
-
Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors
-
doi:10.1021/ci100324n
-
Langelaan DN, Wieczorek M, Blouin C, Rainey JK (2010) Improved helix and kink characterization in membrane proteins allows evaluation of kink sequence predictors. J Chem Inf Model 50(12):2213-2220. doi:10.1021/ci100324n
-
(2010)
J Chem Inf Model
, vol.50
, Issue.12
, pp. 2213-2220
-
-
Langelaan, D.N.1
Wieczorek, M.2
Blouin, C.3
Rainey, J.K.4
-
24
-
-
79959336987
-
TMKink: A method to predict transmembrane helix kinks
-
doi:10.1002/pro.653
-
Meruelo AD, Samish I, Bowie JU (2011) TMKink: a method to predict transmembrane helix kinks. Protein Sci 20(7):1256-1264. doi:10.1002/pro.653
-
(2011)
Protein Sci
, vol.20
, Issue.7
, pp. 1256-1264
-
-
Meruelo, A.D.1
Samish, I.2
Bowie, J.U.3
-
25
-
-
82355168443
-
String kernels and high-quality data set for improved prediction of kinked helices in alpha-helical membrane proteins
-
doi:10.1021/ci200278w
-
Kneissl B, Mueller SC, Tautermann CS, Hildebrandt A (2011) String kernels and high-quality data set for improved prediction of kinked helices in alpha-helical membrane proteins. J Chem Inf Model 51(11):3017-3025. doi:10.1021/ci200278w
-
(2011)
J Chem Inf Model
, vol.51
, Issue.11
, pp. 3017-3025
-
-
Kneissl, B.1
Mueller, S.C.2
Tautermann, C.S.3
Hildebrandt, A.4
-
26
-
-
84863106674
-
Replica exchange Monte- Carlo simulations of helix bundle membrane proteins: Rotational parameters of helices
-
doi:10.1007/s10822-012-9562-1
-
Wu HH, Chen CC, Chen CM (2012) Replica exchange Monte- Carlo simulations of helix bundle membrane proteins: rotational parameters of helices. J Comput Aided Mol Des 26(3):363-374. doi:10.1007/s10822-012-9562-1
-
(2012)
J Comput Aided Mol des
, vol.26
, Issue.3
, pp. 363-374
-
-
Wu, H.H.1
Chen, C.C.2
Chen, C.M.3
-
27
-
-
0043180474
-
PISCES: A protein sequence culling server
-
Wang G, Dunbrack RL Jr (2003) PISCES: a protein sequence culling server. Bioinformatics 19(12):1589-1591
-
(2003)
Bioinformatics
, vol.19
, Issue.12
, pp. 1589-1591
-
-
Wang, G.1
Dunbrack Jr., R.L.2
-
28
-
-
10944245838
-
A method for structural analysis of alpha-helices of membrane proteins
-
-):. doi:10.1007/s00894-004-0212-y
-
Mohapatra PK, Khamari A, Raval MK (2004) A method for structural analysis of alpha-helices of membrane proteins. J Mol Model 10(5-6):393-398. doi:10.1007/s00894-004-0212-y
-
(2004)
J Mol Model
, vol.10
, Issue.5-6
, pp. 393-398
-
-
Mohapatra, P.K.1
Khamari, A.2
Raval, M.K.3
-
29
-
-
0037441653
-
Structure validation by Calpha geometry: Phi, psi and Cbeta deviation
-
doi:10.1002/prot.10286
-
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50(3):437-450. doi:10.1002/prot.10286
-
(2003)
Proteins
, vol.50
, Issue.3
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
De Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
30
-
-
22544450619
-
Molecular dynamics study of a membrane-water interface
-
Zhou F, Schulten K (1995) Molecular dynamics study of a membrane-water interface. J Phys Chem 99(7):2194-2207
-
(1995)
J Phys Chem
, vol.99
, Issue.7
, pp. 2194-2207
-
-
Zhou, F.1
Schulten, K.2
-
31
-
-
0025310046
-
Electrical modulation of membrane proteins: Enforced conformational oscillations and biological energy and signal transductions
-
doi:10.1146/annurev.bb.19.060190.000503
-
Tsong TY (1990) Electrical modulation of membrane proteins: enforced conformational oscillations and biological energy and signal transductions. Annu Rev Biophys Biophys Chem 19:83-106. doi:10.1146/annurev.bb.19.060190.000503
-
(1990)
Annu Rev Biophys Biophys Chem
, vol.19
, pp. 83-106
-
-
Tsong, T.Y.1
-
32
-
-
17144410761
-
Thermostat algorithms for molecular dynamics simulations
-
doi: 10.1007/B99427
-
Hunenberger P (2005) Thermostat algorithms for molecular dynamics simulations. Adv Polym Sci 173:105-147. doi: 10.1007/B99427
-
(2005)
Adv Polym Sci
, vol.173
, pp. 105-147
-
-
Hunenberger, P.1
-
33
-
-
1942519275
-
SPICKER: A clustering approach to identify near-native protein folds
-
Zhang Y, Skolnick J (2004) SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 25(6):865-871
-
(2004)
J Comput Chem
, vol.25
, Issue.6
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
34
-
-
0015859467
-
Principles that govern the folding of protein chains
-
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(96):223-230
-
(1973)
Science
, vol.181
, Issue.96
, pp. 223-230
-
-
Anfinsen, C.B.1
-
35
-
-
0032530578
-
Clustering of low-energy conformations near the native structures of small proteins
-
Shortle D, Simons KT, Baker D (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc Natl Acad Sci USA 95(19):11158-11162
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, Issue.19
, pp. 11158-11162
-
-
Shortle, D.1
Simons, K.T.2
Baker, D.3
-
36
-
-
0032552880
-
The preference of tryptophan for membrane interfaces
-
doi:10.1021/bi980809c
-
Yau WM, Wimley WC, Gawrisch K, White SH (1998) The preference of tryptophan for membrane interfaces. Biochemistry 37(42):14713-14718. doi:10.1021/bi980809c
-
(1998)
Biochemistry
, vol.37
, Issue.42
, pp. 14713-14718
-
-
Yau, W.M.1
Wimley, W.C.2
Gawrisch, K.3
White, S.H.4
-
37
-
-
0032817780
-
Helix packing in polytopic membrane proteins: Role of glycine in transmembrane helix association
-
doi:10.1016/S0006-3495(99)77009-8
-
Javadpour MM, Eilers M, Groesbeek M, Smith SO (1999) Helix packing in polytopic membrane proteins: role of glycine in transmembrane helix association. Biophys J 77(3):1609-1618. doi:10.1016/S0006-3495(99)77009-8
-
(1999)
Biophys J
, vol.77
, Issue.3
, pp. 1609-1618
-
-
Javadpour, M.M.1
Eilers, M.2
Groesbeek, M.3
Smith, S.O.4
-
38
-
-
77955984919
-
Internally bridging water molecule in transmembrane alpha-helical kink
-
doi:10.1016/j.sbi.2010. 05.008
-
Miyano M, Ago H, Saino H, Hori T, Ida K (2010) Internally bridging water molecule in transmembrane alpha-helical kink. Curr Opin Struct Biol 20(4):456-463. doi:10.1016/j.sbi.2010. 05.008
-
(2010)
Curr Opin Struct Biol
, vol.20
, Issue.4
, pp. 456-463
-
-
Miyano, M.1
Ago, H.2
Saino, H.3
Hori, T.4
Ida, K.5
-
39
-
-
0030983047
-
Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria
-
doi:10.1002/pro.5560060407
-
Wallin E, Tsukihara T, Yoshikawa S, von Heijne G, Elofsson A (1997) Architecture of helix bundle membrane proteins: an analysis of cytochrome c oxidase from bovine mitochondria. Protein Sci 6(4):808-815. doi:10.1002/pro. 5560060407
-
(1997)
Protein Sci
, vol.6
, Issue.4
, pp. 808-815
-
-
Wallin, E.1
Tsukihara, T.2
Yoshikawa, S.3
Von Heijne, G.4
Elofsson, A.5
-
40
-
-
80755133615
-
Classification and visualization of the social science network by the minimum span clustering method
-
doi: 10.1002/Asi.21634
-
Chang YF, Chen CM (2011) Classification and visualization of the social science network by the minimum span clustering method. J Am Soc Inform Sci Technol 62(12):2404-2413. doi: 10.1002/Asi.21634
-
(2011)
J Am Soc Inform Sci Technol
, vol.62
, Issue.12
, pp. 2404-2413
-
-
Chang, Y.F.1
Chen, C.M.2
-
41
-
-
17644392830
-
TM-align: A protein structure alignment algorithm based on the TM-score
-
doi:10.1093/nar/gki524
-
Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33(7):2302-2309. doi:10.1093/nar/gki524
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.7
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
42
-
-
0033670439
-
MaxSub: An automated measure for the assessment of protein structure prediction quality
-
Siew N, Elofsson A, Rychlewski L, Fischer D (2000) MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 16(9):776-785
-
(2000)
Bioinformatics
, vol.16
, Issue.9
, pp. 776-785
-
-
Siew, N.1
Elofsson, A.2
Rychlewski, L.3
Fischer, D.4
-
43
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zemla A (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 31(13):3370-3374
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3370-3374
-
-
Zemla, A.1
-
44
-
-
0025249842
-
Membrane protein folding and oligomerization: The two-stage model
-
Popot JL, Engelman DM (1990) Membrane protein folding and oligomerization: the two-stage model. Biochemistry 29(17): 4031-4037
-
(1990)
Biochemistry
, vol.29
, Issue.17
, pp. 4031-4037
-
-
Popot, J.L.1
Engelman, D.M.2
-
45
-
-
0026642866
-
Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment
-
Kahn TW, Engelman DM (1992) Bacteriorhodopsin can be refolded from two independently stable transmembrane helices and the complementary five-helix fragment. Biochemistry 31(26):6144-6151
-
(1992)
Biochemistry
, vol.31
, Issue.26
, pp. 6144-6151
-
-
Kahn, T.W.1
Engelman, D.M.2
-
46
-
-
0030003278
-
Co assembly of synthetic segments of shaker K+ channel within phospholipid membranes
-
doi: 10.1021/bi952988t
-
Peled-Zehavi H, Arkin IT, Engelman DM, Shai Y (1996) Co assembly of synthetic segments of shaker K+ channel within phospholipid membranes. Biochemistry 35(21):6828-6838. doi: 10.1021/bi952988t
-
(1996)
Biochemistry
, vol.35
, Issue.21
, pp. 6828-6838
-
-
Peled-Zehavi, H.1
Arkin, I.T.2
Engelman, D.M.3
Shai, Y.4
|