-
1
-
-
65549083717
-
Gridmat-md: a grid-based membrane analysis tool for use with molecular dynamics
-
Allen, W. J., Lemkul, J. A., and Bevan, D. R. (2009). Gridmat-md: a grid-based membrane analysis tool for use with molecular dynamics. J. Comput. Chem. 30, 1952-1958.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1952-1958
-
-
Allen, W.J.1
Lemkul, J.A.2
Bevan, D.R.3
-
2
-
-
0000550720
-
Strength of hydrogen bonds in α helices
-
Arora, N., and Jayaram, B. (1996). Strength of hydrogen bonds in α helices. J. Comput. Chem. 18, 1245-1252.
-
(1996)
J. Comput. Chem.
, vol.18
, pp. 1245-1252
-
-
Arora, N.1
Jayaram, B.2
-
3
-
-
0025825726
-
A novel multigene family may encode odorant receptors: a molecular basis for odor recognition
-
Buck, L., and Axel, R. (1991). A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175-187.
-
(1991)
Cell
, vol.65
, pp. 175-187
-
-
Buck, L.1
Axel, R.2
-
4
-
-
84888005594
-
Hydrophobicity proles in G protein-coupled receptor transmembrane helical domains
-
Crasto, C. (2010). Hydrophobicity proles in G protein-coupled receptor transmembrane helical domains. J. Receptor Ligand Channel Res. 3, 123-133.
-
(2010)
J. Receptor Ligand Channel Res.
, vol.3
, pp. 123-133
-
-
Crasto, C.1
-
5
-
-
0035822998
-
A diverse family of GPCRs expressed in specic subsets of noci-ceptive sensory neurons
-
Dong, X., Han, S. K., Zylka, M. J., Simon, M. I., and Anderson, D. J.(2001). A diverse family of GPCRs expressed in specic subsets of noci-ceptive sensory neurons. Cell 106, 619-632.
-
(2001)
Cell
, vol.106
, pp. 619-632
-
-
Dong, X.1
Han, S.K.2
Zylka, M.J.3
Simon, M.I.4
Anderson, D.J.5
-
6
-
-
0025952856
-
Olfactory impairment in motor neuron disease: a pilot study
-
Elian, M. (1991). Olfactory impairment in motor neuron disease: a pilot study. J. Neurol. Neurosurg. Psychiatr. 54, 927-928.
-
(1991)
J. Neurol. Neurosurg. Psychiatr.
, vol.54
, pp. 927-928
-
-
Elian, M.1
-
7
-
-
43749107283
-
Comparative protein structure modeling with modeller
-
5. 6. 1- 5. 6.
-
Eswar, N., Marti-Renom, M. A., Webb, B., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., and Sali, A. (2006). Comparative protein structure modeling with modeller. Curr. Protoc. Bioinformatics 15, 5.6.1- 5.6.30.
-
(2006)
Curr. Protoc. Bioinformatics
, vol.15
-
-
Eswar, N.1
Marti-Renom, M.A.2
Webb, B.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.6
Pieper, U.7
Sali, A.8
-
8
-
-
0038024615
-
The G-protein-coupled receptors in the human genome form ve main families.Phylogenetic analysis, paralogon groups, and ngerprints
-
Fredriksson, R., Lagerström, M. C., Lundin, L.-G., and Schiöth, H. B. (2003). The G-protein-coupled receptors in the human genome form ve main families.Phylogenetic analysis, paralogon groups, and ngerprints. Mol. Pharmacol. 63, 1256-1272.
-
(2003)
Mol. Pharmacol.
, vol.63
, pp. 1256-1272
-
-
Fredriksson, R.1
Lagerström, M.C.2
Lundin, L.-G.3
Schiöth, H.B.4
-
9
-
-
0037357440
-
Population differences in the human functional olfactory repertoire
-
Gilad,Y., and Lancet,D. (2003). Population differences in the human functional olfactory repertoire.Mol. Biol. Evol. 20, 307-314.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 307-314
-
-
Gilad, Y.1
Lancet, D.2
-
10
-
-
0035001936
-
The complete human olfactory subgenome
-
Glusman, G., Yanai, I., Rubin, I., and Lancet, D. (2001). The complete human olfactory subgenome. Genome Res. 11, 685-702.
-
(2001)
Genome Res
, vol.11
, pp. 685-702
-
-
Glusman, G.1
Yanai, I.2
Rubin, I.3
Lancet, D.4
-
11
-
-
0031984517
-
The many faces of G protein signaling
-
Hamm, H. E. (1998). The many faces of G protein signaling. J. Biol. Chem. 273, 669-672.
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 669-672
-
-
Hamm, H.E.1
-
12
-
-
33645783040
-
Probing a model of a gpcr/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor
-
Hénin, J., Maigret, B., Tarek, M., Escrieut,C., Fourmy,D., and Chipot, C. (2006). Probing a model of a gpcr/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor. Biophys. J. 90, 1232-1240.
-
(2006)
Biophys. J.
, vol.90
, pp. 1232-1240
-
-
Hénin, J.1
Maigret, B.2
Tarek, M.3
Escrieut, C.4
Fourmy, D.5
Chipot, C.6
-
13
-
-
46249092554
-
Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess, B., Kutzner, C., van der Spoel, D., and Lindahl, E. (2008). Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435-447.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
14
-
-
54449098286
-
Structural basis for ligand binding and specificity in adrenergic receptors: implications for GPCR-targeted drug discovery
-
Huber, T., Menon, S., and Sakmar, T. P. (2008). Structural basis for ligand binding and specicity in adrenergic receptors: implications for GPCR-targeted drug discovery. Biochemistry 47, 11013-11023.
-
(2008)
Biochemistry
, vol.47
, pp. 11013-11023
-
-
Huber, T.1
Menon, S.2
Sakmar, T.P.3
-
15
-
-
0029878720
-
VMD - visual molecular dynamics
-
Humphrey, W., Dalke, A., and Schulten, K. (1996). VMD - visual molecular dynamics. J. Mol. Graph. 14, 33-38.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
16
-
-
56749103466
-
The 2.6 angstrom crystalstructure of a human a2a adenosine receptor bound to an antagonist.
-
Jaakola,V. P.,Griffith,M. T.,Hanson,M. A.,Cherezov,V.,Chien, E.Y. T., Lane, J. R., Ijzerman, A. P., and Stevens, R. C. (2008). The 2.6 angstrom crystalstructure of a human a2a adenosine receptor bound to an antagonist. Science 322, 1211-1217.
-
(2008)
Science
, vol.322
, pp. 1211-1217
-
-
Jaakola, V.P.1
Griffith, M.T.2
Hanson, M.A.3
Cherezov, V.4
Chien, E.Y.T.5
Lane, J.R.6
Ijzerman, A.P.7
Stevens, R.C.8
-
17
-
-
77953377650
-
Update of the CHARMM allatom additive force eld for lipids: validation on six lipid types
-
Klauda, J. B., Venable, R. M., Freites, J. A., O'Connor, J. W., Tobias, D. J., Mondragon-Ramirez, C., Vorobyov, I., MacKerell, A. D. Jr., and Pastor, R. W. (2010). Update of the CHARMM allatom additive force eld for lipids: validation on six lipid types. J. Phys. Chem. B 114, 7830-7843.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7830-7843
-
-
Klauda, J.B.1
Venable, R.M.2
Freites, J.A.3
O'Connor, J.W.4
Tobias, D.J.5
Mondragon-Ramirez, C.6
Vorobyov, I.7
MacKerell Jr., A.D.8
Pastor, R.W.9
-
18
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes
-
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E. L. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567-580.
-
(2001)
J. Mol. Biol.
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.L.4
-
19
-
-
27944475233
-
Structural activation pathways from dynamic olfactory receptor-odorant interactions
-
Lai, P. C., Singer, M. S., and Crasto, C. J. (2005). Structural activation pathways from dynamic olfactory receptor-odorant interactions. Chem. Senses 30, 781-792.
-
(2005)
Chem. Senses
, vol.30
, pp. 781-792
-
-
Lai, P.C.1
Singer, M.S.2
Crasto, C.J.3
-
20
-
-
25444478851
-
Molecular dynamics simulations of retinal in rhodopsin: fromthe dark-adapted state towards lumirhodopsin
-
Lemaître, V., Yeagle, P., and Watts, A. (2005). Molecular dynamics simulations of retinal in rhodopsin: fromthe dark-adapted state towards lumirhodopsin. Biochemistry 44, 12667-12680.
-
(2005)
Biochemistry
, vol.44
, pp. 12667-12680
-
-
Lemaître, V.1
Yeagle, P.2
Watts, A.3
-
21
-
-
58149161567
-
The hot-solvent/cold-solute problem revisited
-
Lingenheil,M.,Denschlag, R., Reichold, R., and Tavan, P. (2008). The hot-solvent/cold-solute problem revisited. J. Chem. Theory Comput. 4, 1293-1306.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 1293-1306
-
-
Lingenheil, M.1
Denschlag, R.2
Reichold, R.3
Tavan, P.4
-
22
-
-
0033525727
-
Combinatorial receptor codes for odors
-
Malnic,B.,Hirono, J., Sato,T., and Buck, L. B. (1999). Combinatorial receptor codes for odors. Cell 96, 712-723.
-
(1999)
Cell
, vol.96
, pp. 712-723
-
-
Malnic, B.1
Hirono, J.2
Sato, T.3
Buck, L.B.4
-
23
-
-
22844434585
-
Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system
-
Matarazzo, V., Clot-Faybesse, O., Marcet, B., Guiraudie-Capraz, G., Atanasova, B., Devauchelle, G., Cerutti, M., Etiévant, P., and Ronin, C. (2005). Functional characterization of two human olfactory receptors expressed in the baculovirus Sf9 insect cell system. Chem. Senses 30, 195-207.
-
(2005)
Chem. Senses
, vol.30
, pp. 195-207
-
-
Matarazzo, V.1
Clot-Faybesse, O.2
Marcet, B.3
Guiraudie-Capraz, G.4
Atanasova, B.5
Devauchelle, G.6
Cerutti, M.7
Etiévant, P.8
Ronin, C.9
-
24
-
-
0036797016
-
Porcine odorant-binding protein selectively binds to a human olfactory receptor
-
Matarazzo, V., Zsürger, N., Guillemot, J. C., Clot-Faybesse, O., Botto, J. M., Dal Farra, C., Crowe, M., Demaille, J., Vincent, J. P., Mazella, J., andRonin, C. (2002). Porcine odorant-binding protein selectively binds to a human olfactory receptor. Chem. Senses 27, 691-701.
-
(2002)
Chem. Senses
, vol.27
, pp. 691-701
-
-
Matarazzo, V.1
Zsürger, N.2
Guillemot, J.C.3
Clot-Faybesse, O.4
Botto, J.M.5
Dal Farra, C.6
Crowe, M.7
Demaille, J.8
Vincent, J.P.9
Mazella, J.10
Ronin, C.11
-
25
-
-
0031886320
-
Olfaction in neurodegenerative disease: a meta-analysis of olfactory functioning in Alzheimer's and Parkinson's diseases
-
Mesholam, R. I.,Moberg, P. J.,Mahr, R. N., and Doty, R. L. (1998). Olfaction in neurodegenerative disease: a meta-analysis of olfactory functioning in Alzheimer's and Parkinson's diseases. Arch. Neurol. 55, 85-90.
-
(1998)
Arch. Neurol.
, vol.55
, pp. 85-90
-
-
Mesholam, R.I.1
Moberg, P.J.2
Mahr, R.N.3
Doty, R.L.4
-
26
-
-
0034899781
-
Evaluation of methods for the prediction of membrane spanning regions
-
Möller, S., Croning, M. D. R., and Apweiler, R. (2001). Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17, 646-653.
-
(2001)
Bioinformatics
, vol.17
, pp. 646-653
-
-
Möller, S.1
Croning, M.D.R.2
Apweiler, R.3
-
27
-
-
46149089973
-
Simulations of proteins with inhomogeneous degrees of freedom: the effect of thermostats
-
Mor, A., Ziv, G., and Levy, Y. (2008). Simulations of proteins with inhomogeneous degrees of freedom: the effect of thermostats. J. Comput. Chem. 29, 1992-1998.
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1992-1998
-
-
Mor, A.1
Ziv, G.2
Levy, Y.3
-
28
-
-
0026025953
-
Olfactory dysfunction in Parkinson's disease
-
Murofushi, T., Mizuno, M., Osanai, R., and Hayashida, T. (1991). Olfactory dysfunction in Parkinson's disease. ORL J. Otorhinolaryngol. Relat. Spec. 53, 143-146.
-
(1991)
ORL J. Otorhinolaryngol. Relat. Spec.
, vol.53
, pp. 143-146
-
-
Murofushi, T.1
Mizuno, M.2
Osanai, R.3
Hayashida, T.4
-
29
-
-
80051769266
-
The role of conformational ensembles in ligand recognition in G-protein coupled receptors
-
Niesen, M. J. M., Bhattacharya, S., and Vaidehi, N. (2011). The role of conformational ensembles in ligand recognition in G-protein coupled receptors. J.Am.Chem. Soc. 133, 13197-13204.
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 13197-13204
-
-
Niesen, M.J.M.1
Bhattacharya, S.2
Vaidehi, N.3
-
30
-
-
0142091376
-
Evolution of olfactory receptor genes in the human genome
-
Niimura, Y., and Nei, M. (2003). Evolution of olfactory receptor genes in the human genome. Proc.Natl.Acad. Sci. U.S.A. 100, 12235-12240.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 12235-12240
-
-
Niimura, Y.1
Nei, M.2
-
31
-
-
0035928480
-
Length analyses of mammalian G-protein coupled receptors
-
Otaki, J. M., and Firestein, S. (2001). Length analyses of mammalian G-protein coupled receptors. J. Theor. Biol. 211, 315-327.
-
(2001)
J. Theor. Biol.
, vol.211
, pp. 315-327
-
-
Otaki, J.M.1
Firestein, S.2
-
32
-
-
33947381686
-
The highly conserved dry motif of class a G protein-coupled receptors: beyond the ground state
-
Rovati, G. E., Capra, V., and Neubig, R. R. (2007). The highly conserved dry motif of class a G protein-coupled receptors: beyond the ground state. Mol. Pharmacol. 71, 959-964.
-
(2007)
Mol. Pharmacol.
, vol.71
, pp. 959-964
-
-
Rovati, G.E.1
Capra, V.2
Neubig, R.R.3
-
33
-
-
29244479584
-
Molecular dynamics simulations of bovine rhodopsin: infiuence of protonation states and differentmembrane-mimicking environments
-
Schlegel, B., Sippl, W., and Holtje, H. D. (2005). Molecular dynamics simulations of bovine rhodopsin: infiuence of protonation states and differentmembrane-mimicking environments. J. Mol. Model. 12, 49-64.
-
(2005)
J. Mol. Model.
, vol.12
, pp. 49-64
-
-
Schlegel, B.1
Sippl, W.2
Holtje, H.D.3
-
34
-
-
0034042247
-
Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor
-
Singer, M. S. (2000). Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. Chem. Senses 25, 155-165.
-
(2000)
Chem. Senses
, vol.25
, pp. 155-165
-
-
Singer, M.S.1
-
35
-
-
79952116502
-
Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine a(2a) crystal structures
-
Tebben, A. J., and Schnur, D.M. (2010). Beyond rhodopsin: G protein-coupled receptor structure and modeling incorporating the beta2-adrenergic and adenosine a(2a) crystal structures. Methods Mol. Biol. 672, 359-386.
-
(2010)
Methods Mol. Biol.
, vol.672
, pp. 359-386
-
-
Tebben, A.J.1
Schnur, D.M.2
-
36
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnady, G. E., and Simon, I. (2001). The HMMTOP transmembrane topology prediction server. Bioinformatics 17, 849-850.
-
(2001)
Bioinformatics
, vol.17
, pp. 849-850
-
-
Tusnady, G.E.1
Simon, I.2
-
37
-
-
33646138957
-
Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques
-
Ulmschneider, M. B., Sansom, M. S. P., and Di Nola, A. (2006). Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques. Biophys. J. 90, 1650-1660.
-
(2006)
Biophys. J.
, vol.90
, pp. 1650-1660
-
-
Ulmschneider, M.B.1
Sansom, M.S.P.2
Di Nola, A.3
-
38
-
-
0030248996
-
Low-resolution docking: prediction of complexes for underdetermined structures
-
Vakser, I. A. (1996). Low-resolution docking: prediction of complexes for underdetermined structures. Biopolymers 39, 455-464.
-
(1996)
Biopolymers
, vol.39
, pp. 455-464
-
-
Vakser, I.A.1
-
39
-
-
79551571786
-
Predicting novel bindingmodes of agonists to β adrenergic receptors using allatom molecular dynamics simulations
-
doi:10.1371/journal.pcbi.1001053
-
Vanni, S., Neri, M., Tavernelli, I., and Rothlisberger, U. (2011). Predicting novel bindingmodes of agonists to β adrenergic receptors using allatom molecular dynamics simulations. PLoS Comput. Biol. 7, e1001053. doi:10.1371/journal.pcbi.1001053
-
(2011)
PLoS Comput. Biol.
, vol.7
-
-
Vanni, S.1
Neri, M.2
Tavernelli, I.3
Rothlisberger, U.4
-
40
-
-
76249087938
-
Charmm general force field: a force field for drug-like molecules compatible with the CHARMM allatom additive biological force fields
-
Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., and MacKerell, A. D. Jr. (2010). Charmm general force field: a force field for drug-like molecules compatible with the CHARMM allatom additive biological force fields. J. Comput. Chem. 31, 671-690.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
MacKerell Jr., A.D.11
-
41
-
-
47949129742
-
Structure of a beta1-adrenergic G-protein-coupled receptor
-
Warne, T., Serrano-Vega,M. J., Baker, J. G., Moukhametzianov, R., Edwards, P. C., Henderson, R., Leslie, A. G., Tate, C. G., and Schertler, G. F. (2008). Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454, 486-491.
-
(2008)
Nature
, vol.454
, pp. 486-491
-
-
Warne, T.1
Serrano-Vega, M.J.2
Baker, J.G.3
Moukhametzianov, R.4
Edwards, P.C.5
Henderson, R.6
Leslie, A.G.7
Tate, C.G.8
Schertler, G.F.9
-
42
-
-
0030750453
-
Longitudinal analysis of olfactory decits in HIV infection
-
Westervelt, H. J., McCaffrey, R. J., Cousins, J. P., Wagle, W. A., and Haase, R. F. (1997). Longitudinal analysis of olfactory decits in HIV infection. Arch. Clin. Neuropsychol. 12, 5557-5565.
-
(1997)
Arch. Clin. Neuropsychol.
, vol.12
, pp. 5557-5565
-
-
Westervelt, H.J.1
McCaffrey, R.J.2
Cousins, J.P.3
Wagle, W.A.4
Haase, R.F.5
-
43
-
-
77954256616
-
g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation
-
Wolf, M. G., Hoefiing, M., Aponte-Santamaria, C., Grubmüller,H., and Groenhof, G. (2010). g_membed: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation. J. Comput. Chem. 31, 2169-2174.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 2169-2174
-
-
Wolf, M.G.1
Hoeing, M.2
Aponte-Santamaria, C.3
Grubmüller, H.4
Groenhof, G.5
-
44
-
-
21044437346
-
Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system
-
Zhang, Y., Sham, Y. Y., Rajamani, R., Gao, J., and Portoghese, P. S. (2005). Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane-aqueous system. Chembiochem 6, 853-859.
-
(2005)
Chembiochem
, vol.6
, pp. 853-859
-
-
Zhang, Y.1
Sham, Y.Y.2
Rajamani, R.3
Gao, J.4
Portoghese, P.S.5
-
45
-
-
0035237870
-
The human olfactory receptor repertoire
-
research0018.1-research0018.12
-
Zozulya, S., Echeverri, F., and Nguyen, T. (2001). The human olfactory receptor repertoire. Genome Biol. 2, research0018.1-research0018.12
-
(2001)
Genome Biol.
, vol.2
-
-
Zozulya, S.1
Echeverri, F.2
Nguyen, T.3
|