-
1
-
-
84976540768
-
GPCRdb: the G protein‐coupled receptor database – an introduction
-
Munk, C., Isberg, V., Mordalski, S., Harpsøe, K., Rataj, K., Hauser, A.S., Kolb, P., Bojarski, A.J., Vriend, G., Gloriam, D.E., GPCRdb: the G protein‐coupled receptor database – an introduction. Br J Pharmacol 173 (2016), 2195–2207.
-
(2016)
Br J Pharmacol
, vol.173
, pp. 2195-2207
-
-
Munk, C.1
Isberg, V.2
Mordalski, S.3
Harpsøe, K.4
Rataj, K.5
Hauser, A.S.6
Kolb, P.7
Bojarski, A.J.8
Vriend, G.9
Gloriam, D.E.10
-
2
-
-
85035315619
-
Trends in GPCR drug discovery: new agents, targets and indications
-
Hauser, A.S., Attwood, M.M., Rask-Andersen, M., Schiöth, H.B., Gloriam, D.E., Trends in GPCR drug discovery: new agents, targets and indications. Nat Rev Drug Discov 16 (2017), 829–842.
-
(2017)
Nat Rev Drug Discov
, vol.16
, pp. 829-842
-
-
Hauser, A.S.1
Attwood, M.M.2
Rask-Andersen, M.3
Schiöth, H.B.4
Gloriam, D.E.5
-
3
-
-
85019554528
-
Selectivity determinants of GPCR–G-protein binding
-
Flock, T., Hauser, A.S., Lund, N., Gloriam, D.E., Balaji, S., Babu, M.M., Selectivity determinants of GPCR–G-protein binding. Nature 545 (2017), 317–322.
-
(2017)
Nature
, vol.545
, pp. 317-322
-
-
Flock, T.1
Hauser, A.S.2
Lund, N.3
Gloriam, D.E.4
Balaji, S.5
Babu, M.M.6
-
4
-
-
85049245029
-
How the ubiquitous GPCR receptor family selectively activates signalling pathways
-
Capper, M.J., Wacker, D., How the ubiquitous GPCR receptor family selectively activates signalling pathways. Nature 558 (2018), 529–530.
-
(2018)
Nature
, vol.558
, pp. 529-530
-
-
Capper, M.J.1
Wacker, D.2
-
5
-
-
0028174033
-
Fingerprinting G-protein-coupled receptors
-
Attwood, T.K., Findlay, J.B., Fingerprinting G-protein-coupled receptors. Protein Eng Des Sel 7 (1994), 195–203.
-
(1994)
Protein Eng Des Sel
, vol.7
, pp. 195-203
-
-
Attwood, T.K.1
Findlay, J.B.2
-
6
-
-
0028338534
-
GCRDb: a G-protein-coupled receptor database
-
Kolakowski, J.L., GCRDb: a G-protein-coupled receptor database. Receptors Channels 2 (1994), 1–7.
-
(1994)
Receptors Channels
, vol.2
, pp. 1-7
-
-
Kolakowski, J.L.1
-
7
-
-
0038024615
-
The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
-
Fredriksson, R., Lagerström, M.C., Lundin, L.G., Schiöth, H.B., The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63 (2003), 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
-
8
-
-
0037252680
-
GPCRdb information system for G protein-coupled receptors
-
Horn, F., Bettler, E., Oliveira, L., Campagne, F., Cohen, F.E., Vriend, G., GPCRdb information system for G protein-coupled receptors. Nucleic Acids Res 31 (2003), 294–297.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 294-297
-
-
Horn, F.1
Bettler, E.2
Oliveira, L.3
Campagne, F.4
Cohen, F.E.5
Vriend, G.6
-
9
-
-
80052158550
-
Independent HHsearch, Needleman–Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families
-
Nordström, K.J., Sällman Almén, M., Edstam, M.M., Fredriksson, R., Schiöth, H.B., Independent HHsearch, Needleman–Wunsch-based, and motif analyses reveal the overall hierarchy for most of the G protein-coupled receptor families. Mol Biol Evol 28 (2011), 2471–2480.
-
(2011)
Mol Biol Evol
, vol.28
, pp. 2471-2480
-
-
Nordström, K.J.1
Sällman Almén, M.2
Edstam, M.M.3
Fredriksson, R.4
Schiöth, H.B.5
-
10
-
-
84951743686
-
Comparing Class A GPCRs to bitter taste receptors: structural motifs, ligand interactions and agonist-to-antagonist ratios
-
A.K. Shukla Academic Press Comparison of human bitter taste receptors (hTAS2Rs) with class A GPCRs, based not only on the conservation of sequence and structural motifs, but also conservation of ligand binding residues. The results support the classification of hTAS2Rs as class A GPCRs.
-
Di Pizio, A., Levit, A., Slutzki, M., Behrens, M., Karaman, R., Niv, M.Y., Comparing Class A GPCRs to bitter taste receptors: structural motifs, ligand interactions and agonist-to-antagonist ratios. Shukla, A.K., (eds.) Methods in Cell Biology, vol 132, 2016, Academic Press, 401–427 Comparison of human bitter taste receptors (hTAS2Rs) with class A GPCRs, based not only on the conservation of sequence and structural motifs, but also conservation of ligand binding residues. The results support the classification of hTAS2Rs as class A GPCRs.
-
(2016)
Methods in Cell Biology
, vol.132
, pp. 401-427
-
-
Di Pizio, A.1
Levit, A.2
Slutzki, M.3
Behrens, M.4
Karaman, R.5
Niv, M.Y.6
-
11
-
-
85034078770
-
Agonist binding to chemosensory receptors: a systematic bioinformatics analysis
-
A systematic bioinformatics study across the human bitter taste and olfactory receptors with available experimental data (as of August 2017) shows the limited predictive power of the bioinformatics combined with docking. Significant improvement can be achieved by subsequent molecular dynamics simulations.
-
Fierro, F., Suku, E., Alfonso-Prieto, M., Giorgetti, A., Cichon, S., Carloni, P., Agonist binding to chemosensory receptors: a systematic bioinformatics analysis. Front Mol Biosci, 4, 2017, 63 A systematic bioinformatics study across the human bitter taste and olfactory receptors with available experimental data (as of August 2017) shows the limited predictive power of the bioinformatics combined with docking. Significant improvement can be achieved by subsequent molecular dynamics simulations.
-
(2017)
Front Mol Biosci
, vol.4
, pp. 63
-
-
Fierro, F.1
Suku, E.2
Alfonso-Prieto, M.3
Giorgetti, A.4
Cichon, S.5
Carloni, P.6
-
12
-
-
85054450985
-
Structural and druggability landscape of Frizzled G protein-coupled receptors
-
Zhang, X., Dong, S., Xu, F., Structural and druggability landscape of Frizzled G protein-coupled receptors. Trends Biochem Sci 43 (2018), P1033–P1046.
-
(2018)
Trends Biochem Sci
, vol.43
, pp. P1033-P1046
-
-
Zhang, X.1
Dong, S.2
Xu, F.3
-
13
-
-
84873685831
-
Molecular signatures of G-protein-coupled receptors
-
Venkatakrishnan, A.J., Deupi, X., Lebon, G., Tate, C.G., Schertler, G.F., Babu, M.M., Molecular signatures of G-protein-coupled receptors. Nature 494 (2013), 185–194.
-
(2013)
Nature
, vol.494
, pp. 185-194
-
-
Venkatakrishnan, A.J.1
Deupi, X.2
Lebon, G.3
Tate, C.G.4
Schertler, G.F.5
Babu, M.M.6
-
14
-
-
84979780638
-
Integrating structural and mutagenesis data to elucidate GPCR ligand binding
-
Munk, C., Harpsøe, K., Hauser, A.S., Isberg, V., Gloriam, D.E., Integrating structural and mutagenesis data to elucidate GPCR ligand binding. Curr Opin Pharmacol 30 (2016), 51–58.
-
(2016)
Curr Opin Pharmacol
, vol.30
, pp. 51-58
-
-
Munk, C.1
Harpsøe, K.2
Hauser, A.S.3
Isberg, V.4
Gloriam, D.E.5
-
15
-
-
84925852119
-
Regulation of the oncoprotein smoothened by small molecules
-
Sharpe, H.J., Wang, W., Hannoush, R.N., De Sauvage, F.J., Regulation of the oncoprotein smoothened by small molecules. Nat Chem Biol 11 (2015), 246–255.
-
(2015)
Nat Chem Biol
, vol.11
, pp. 246-255
-
-
Sharpe, H.J.1
Wang, W.2
Hannoush, R.N.3
De Sauvage, F.J.4
-
16
-
-
85049584126
-
Mechanisms of Wnt signaling and control
-
Grainger, S., Willert, K., Mechanisms of Wnt signaling and control. Wiley Interdiscip Rev Syst Biol Med, 30, 2018, e1422.
-
(2018)
Wiley Interdiscip Rev Syst Biol Med
, vol.30
-
-
Grainger, S.1
Willert, K.2
-
17
-
-
84961960745
-
Bitter taste receptors: extraoral roles in pathophysiology
-
Shaik, F.A., Singh, N., Arakawa, M., Duan, K., Bhullar, R.P., Chelikani, P., Bitter taste receptors: extraoral roles in pathophysiology. Int J Biochem Cell Biol 77 (2016), 197–204.
-
(2016)
Int J Biochem Cell Biol
, vol.77
, pp. 197-204
-
-
Shaik, F.A.1
Singh, N.2
Arakawa, M.3
Duan, K.4
Bhullar, R.P.5
Chelikani, P.6
-
18
-
-
85012918828
-
Extraoral bitter taste receptors in health and disease
-
Lu, P., Zhang, C.H., Lifshitz, L.M., ZhuGe, R., Extraoral bitter taste receptors in health and disease. J Gen Physiol 149 (2017), 181–197.
-
(2017)
J Gen Physiol
, vol.149
, pp. 181-197
-
-
Lu, P.1
Zhang, C.H.2
Lifshitz, L.M.3
ZhuGe, R.4
-
19
-
-
85057608290
-
Therapeutic potential of ectopic olfactory and taste receptors
-
Lee, S.J., Depoortere, I., Hatt, H., Therapeutic potential of ectopic olfactory and taste receptors. Nat Rev Drug Discov 18 (2019), 116–138.
-
(2019)
Nat Rev Drug Discov
, vol.18
, pp. 116-138
-
-
Lee, S.J.1
Depoortere, I.2
Hatt, H.3
-
20
-
-
84899654206
-
Targeting of smoothened for therapeutic gain
-
Ruat, M., Hoch, L., Faure, H., Rognan, D., Targeting of smoothened for therapeutic gain. Trends Pharmacol Sci 35 (2014), 237–246.
-
(2014)
Trends Pharmacol Sci
, vol.35
, pp. 237-246
-
-
Ruat, M.1
Hoch, L.2
Faure, H.3
Rognan, D.4
-
21
-
-
85020025659
-
Wnt/β-catenin signaling, disease, and emerging therapeutic modalities
-
Nusse, R., Clevers, H., Wnt/β-catenin signaling, disease, and emerging therapeutic modalities. Cell 169 (2017), 985–999.
-
(2017)
Cell
, vol.169
, pp. 985-999
-
-
Nusse, R.1
Clevers, H.2
-
22
-
-
84982728617
-
Structural basis of smoothened regulation by its extracellular domains
-
This elegant, multidisciplinary study, combining X-ray crystallography, in vitro signaling assays, ligand affinity chromatography, pull-down assays and molecular dynamics, proposes that cholesterol acts as an endogenous hSMO modulator by binding to the CRD. Moreover, the simulations show that CRD flexibility is decreased in the presence of cholesterol, suggesting that stabilization of the CRD is connected to receptor activation; this MD-based prediction is supported by additional mutagenesis experiments.
-
Byrne, E.F., Sircar, R., Miller, P.S., Hedger, G., Luchetti, G., Nachtergaele, S., Tully, M.D., Mydock-McGrane, L., Covey, D.F., Rambo, R.P., et al. Structural basis of smoothened regulation by its extracellular domains. Nature 535 (2016), 517–522 This elegant, multidisciplinary study, combining X-ray crystallography, in vitro signaling assays, ligand affinity chromatography, pull-down assays and molecular dynamics, proposes that cholesterol acts as an endogenous hSMO modulator by binding to the CRD. Moreover, the simulations show that CRD flexibility is decreased in the presence of cholesterol, suggesting that stabilization of the CRD is connected to receptor activation; this MD-based prediction is supported by additional mutagenesis experiments.
-
(2016)
Nature
, vol.535
, pp. 517-522
-
-
Byrne, E.F.1
Sircar, R.2
Miller, P.S.3
Hedger, G.4
Luchetti, G.5
Nachtergaele, S.6
Tully, M.D.7
Mydock-McGrane, L.8
Covey, D.F.9
Rambo, R.P.10
-
23
-
-
84930867918
-
Computational studies of smell and taste receptors
-
Di Pizio, A., Niv, M.Y., Computational studies of smell and taste receptors. Isr J Chem 54 (2014), 1205–1218.
-
(2014)
Isr J Chem
, vol.54
, pp. 1205-1218
-
-
Di Pizio, A.1
Niv, M.Y.2
-
24
-
-
85059799078
-
BitterDB: taste ligands and receptors database in 2019
-
Dagan-Wiener, A., Di Pizio, A., Nissim, I., Bahia, M.S., Dubovski, N., Margulis, E., Niv, M.Y., BitterDB: taste ligands and receptors database in 2019. Nucleic Acids Res 47 (2019), D1179–D1185.
-
(2019)
Nucleic Acids Res
, vol.47
, pp. D1179-D1185
-
-
Dagan-Wiener, A.1
Di Pizio, A.2
Nissim, I.3
Bahia, M.S.4
Dubovski, N.5
Margulis, E.6
Niv, M.Y.7
-
26
-
-
0035935802
-
Calculating free energies using average force
-
Darve, E., Pohorille, A., Calculating free energies using average force. J Chem Phys 115 (2001), 9169–9183.
-
(2001)
J Chem Phys
, vol.115
, pp. 9169-9183
-
-
Darve, E.1
Pohorille, A.2
-
27
-
-
16444385400
-
Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid
-
Torrie, G.M., Valleau, J.P., Monte Carlo free energy estimates using non-Boltzmann sampling: application to the sub-critical Lennard-Jones fluid. Chem Phys Lett 28 (1974), 578–581.
-
(1974)
Chem Phys Lett
, vol.28
, pp. 578-581
-
-
Torrie, G.M.1
Valleau, J.P.2
-
28
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33 (2000), 889–897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
-
29
-
-
84899786103
-
Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation
-
Bai, Q., Shen, Y., Jin, N., Liu, H., Yao, X., Molecular modeling study on the dynamical structural features of human smoothened receptor and binding mechanism of antagonist LY2940680 by metadynamics simulation and free energy calculation. Biochim Biophys Acta Gen Subj 1840 (2014), 2128–2138.
-
(2014)
Biochim Biophys Acta Gen Subj
, vol.1840
, pp. 2128-2138
-
-
Bai, Q.1
Shen, Y.2
Jin, N.3
Liu, H.4
Yao, X.5
-
30
-
-
84976299535
-
Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions
-
Baltoumas, F.A., Theodoropoulou, M.C., Hamodrakas, S.J., Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions. J Comput Aided Mol Des 30 (2016), 489–512.
-
(2016)
J Comput Aided Mol Des
, vol.30
, pp. 489-512
-
-
Baltoumas, F.A.1
Theodoropoulou, M.C.2
Hamodrakas, S.J.3
-
31
-
-
85019947839
-
Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand
-
This study provides information about the dynamics of the hSMO receptor in complex with cholesterol by combining X-ray crystallography, hydrogen-deuterium exchange analysis and molecular dynamics, further supporting the conclusions of a previous study [22].
-
Zhang, X., Zhao, F., Wu, Y., Yang, J., Han, G.W., Zhao, S., Ishchenko, A., Ye, L., Lin, X., Ding, K., Dharmarajan, V., Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand. Nat Comm, 8, 2017, 15383 This study provides information about the dynamics of the hSMO receptor in complex with cholesterol by combining X-ray crystallography, hydrogen-deuterium exchange analysis and molecular dynamics, further supporting the conclusions of a previous study [22].
-
(2017)
Nat Comm
, vol.8
-
-
Zhang, X.1
Zhao, F.2
Wu, Y.3
Yang, J.4
Han, G.W.5
Zhao, S.6
Ishchenko, A.7
Ye, L.8
Lin, X.9
Ding, K.10
Dharmarajan, V.11
-
32
-
-
84997107840
-
A molecular dynamics approach to identify an oxysterol-based hedgehog pathway inhibitor
-
An arsenal of computational tools is used to investigate the binding modes of oxysterols to the cysteine rich domain (CRD) of the human smoothened receptor (hSMO). The computational results, validated against in vitro functional assays, show that oxysterols can be classified as agonists or antagonists based on their calculated affinity.
-
Dash, R.C., Maschinot, C.R., Hadden, M.K., A molecular dynamics approach to identify an oxysterol-based hedgehog pathway inhibitor. Biochim Biophys Acta Gen Subj 1861 (2017), 168–177 An arsenal of computational tools is used to investigate the binding modes of oxysterols to the cysteine rich domain (CRD) of the human smoothened receptor (hSMO). The computational results, validated against in vitro functional assays, show that oxysterols can be classified as agonists or antagonists based on their calculated affinity.
-
(2017)
Biochim Biophys Acta Gen Subj
, vol.1861
, pp. 168-177
-
-
Dash, R.C.1
Maschinot, C.R.2
Hadden, M.K.3
-
33
-
-
85029484530
-
Deciphering structural stability and binding mechanisms of potential antagonists with smoothened protein
-
Sinha, N., Chowdhury, S., Sarkar, R.R., Deciphering structural stability and binding mechanisms of potential antagonists with smoothened protein. J Biomol Struct Dyn 36 (2018), 2917–2937.
-
(2018)
J Biomol Struct Dyn
, vol.36
, pp. 2917-2937
-
-
Sinha, N.1
Chowdhury, S.2
Sarkar, R.R.3
-
34
-
-
85035245035
-
Molecular modeling study on resistance of WT/D473H SMO to antagonists LDE-225 and LEQ-506
-
Molecular docking, molecular dynamics and free energy calculations help to rationalize the effect of a drug-resistant mutation on the binding of two different hSMO inhibitors. This study may pave the way for future drug design efforts.
-
Tu, J., Li, J.J., Song, L.T., Zhai, H.L., Wang, J., Zhang, X.Y., Molecular modeling study on resistance of WT/D473H SMO to antagonists LDE-225 and LEQ-506. Pharmacol Res 129 (2018), 491–499 Molecular docking, molecular dynamics and free energy calculations help to rationalize the effect of a drug-resistant mutation on the binding of two different hSMO inhibitors. This study may pave the way for future drug design efforts.
-
(2018)
Pharmacol Res
, vol.129
, pp. 491-499
-
-
Tu, J.1
Li, J.J.2
Song, L.T.3
Zhai, H.L.4
Wang, J.5
Zhang, X.Y.6
-
35
-
-
85052890948
-
Structural and dynamic characterization of human Wnt2-Fzd7 complex using computational approaches
-
Kalhor, H., Poorebrahim, M., Rahimi, H., Shabani, A.A., Karimipoor, M., Eidgahi, M.R., Teimoori-Toolabi, L., Structural and dynamic characterization of human Wnt2-Fzd7 complex using computational approaches. J Mol Model, 24, 2018, 274.
-
(2018)
J Mol Model
, vol.24
, pp. 274
-
-
Kalhor, H.1
Poorebrahim, M.2
Rahimi, H.3
Shabani, A.A.4
Karimipoor, M.5
Eidgahi, M.R.6
Teimoori-Toolabi, L.7
-
36
-
-
85052670328
-
Crystal structure of the frizzled 4 receptor in a ligand-free state
-
An excellent study which combines X-ray crystallography with molecular dynamics simulations and in vitro activity assays. It provides hints on the conformational changes occurring upon activation of the frizzled receptor FDZ4.
-
Yang, S., Wu, Y., Xu, T.H., de Waal, P.W., He, Y., Pu, M., Chen, Y., DeBruine, Z.J., Zhang, B., Zaidi, S.A., Popov, P., Crystal structure of the frizzled 4 receptor in a ligand-free state. Nature 560 (2018), 666–670 An excellent study which combines X-ray crystallography with molecular dynamics simulations and in vitro activity assays. It provides hints on the conformational changes occurring upon activation of the frizzled receptor FDZ4.
-
(2018)
Nature
, vol.560
, pp. 666-670
-
-
Yang, S.1
Wu, Y.2
Xu, T.H.3
de Waal, P.W.4
He, Y.5
Pu, M.6
Chen, Y.7
DeBruine, Z.J.8
Zhang, B.9
Zaidi, S.A.10
Popov, P.11
-
37
-
-
85060034904
-
Cholesterol interaction sites on the transmembrane domain of the hedgehog signal transducer and class F G protein-coupled receptor Smoothened
-
Hedger, G., Koldsoe, H., Chavent, M., Siebold, C., Rohatgi, R., Sansom, M., Cholesterol interaction sites on the transmembrane domain of the hedgehog signal transducer and class F G protein-coupled receptor Smoothened. Structure 27 (2019), 549–559.
-
(2019)
Structure
, vol.27
, pp. 549-559
-
-
Hedger, G.1
Koldsoe, H.2
Chavent, M.3
Siebold, C.4
Rohatgi, R.5
Sansom, M.6
-
38
-
-
84941145251
-
Evidence for a transient additional ligand binding site in the TAS2R46 bitter taste receptor
-
Hybrid MM/CG simulations on hTAS2R46, consistent with mutagenesis and functional experiments, suggest the presence of a “two-state” binding architecture able to discriminate highly diverse agonists.
-
Sandal, M., Behrens, M., Brockhoff, A., Musiani, F., Giorgetti, A., Carloni, P., Meyerhof, W., Evidence for a transient additional ligand binding site in the TAS2R46 bitter taste receptor. J Chem Theory Comput 11 (2015), 4439–4449 Hybrid MM/CG simulations on hTAS2R46, consistent with mutagenesis and functional experiments, suggest the presence of a “two-state” binding architecture able to discriminate highly diverse agonists.
-
(2015)
J Chem Theory Comput
, vol.11
, pp. 4439-4449
-
-
Sandal, M.1
Behrens, M.2
Brockhoff, A.3
Musiani, F.4
Giorgetti, A.5
Carloni, P.6
Meyerhof, W.7
-
39
-
-
85030162089
-
Insights into the binding of agonist and antagonist to TAS2R16 receptor: a molecular simulation study
-
Chen, Z., Dong, S., Meng, F., Liang, Y., Zhang, S., Sun, J., Insights into the binding of agonist and antagonist to TAS2R16 receptor: a molecular simulation study. Mol Simul 44 (2018), 322–329.
-
(2018)
Mol Simul
, vol.44
, pp. 322-329
-
-
Chen, Z.1
Dong, S.2
Meng, F.3
Liang, Y.4
Zhang, S.5
Sun, J.6
-
40
-
-
85041678601
-
Plasticity of the ligand binding pocket in the bitter taste receptor T2R7
-
Liu, K., Jaggupilli, A., Premnath, D., Chelikani, P., Plasticity of the ligand binding pocket in the bitter taste receptor T2R7. Biochim Biophys Acta Biomembr 1860 (2018), 991–999.
-
(2018)
Biochim Biophys Acta Biomembr
, vol.1860
, pp. 991-999
-
-
Liu, K.1
Jaggupilli, A.2
Premnath, D.3
Chelikani, P.4
-
41
-
-
85059234847
-
Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics
-
Jaggupilli, A., Singh, N., De Jesus, V.C., Gounni, M.S., Dhanaraj, P., Chelikani, P., Chemosensory bitter taste receptors (T2Rs) are activated by multiple antibiotics. FASEB J 33 (2018), 501–517.
-
(2018)
FASEB J
, vol.33
, pp. 501-517
-
-
Jaggupilli, A.1
Singh, N.2
De Jesus, V.C.3
Gounni, M.S.4
Dhanaraj, P.5
Chelikani, P.6
-
42
-
-
84878112106
-
Structure of the human smoothened receptor bound to an antitumour agent
-
Wang, C., Wu, H., Katritch, V., Han, G.W., Huang, X.P., Liu, W., Siu, F.Y., Roth, B.L., Cherezov, V., Stevens, R.C., Structure of the human smoothened receptor bound to an antitumour agent. Nature 497 (2013), 338–343.
-
(2013)
Nature
, vol.497
, pp. 338-343
-
-
Wang, C.1
Wu, H.2
Katritch, V.3
Han, G.W.4
Huang, X.P.5
Liu, W.6
Siu, F.Y.7
Roth, B.L.8
Cherezov, V.9
Stevens, R.C.10
-
44
-
-
85016149075
-
Protein–ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling
-
Bernetti, M., Cavalli, A., Mollica, L., Protein–ligand (un)binding kinetics as a new paradigm for drug discovery at the crossroad between experiments and modelling. MedChemComm 8 (2017), 534–550.
-
(2017)
MedChemComm
, vol.8
, pp. 534-550
-
-
Bernetti, M.1
Cavalli, A.2
Mollica, L.3
-
45
-
-
85017158247
-
Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations
-
Casasnovas, R., Limongelli, V., Tiwary, P., Carloni, P., Parrinello, M., Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations. J Am Chem Soc 139 (2017), 4780–4788.
-
(2017)
J Am Chem Soc
, vol.139
, pp. 4780-4788
-
-
Casasnovas, R.1
Limongelli, V.2
Tiwary, P.3
Carloni, P.4
Parrinello, M.5
-
46
-
-
85001130088
-
Cholesterol activates the G-protein coupled receptor smoothened to promote hedgehog signaling
-
Luchetti, G., Sircar, R., Kong, J.H., Nachtergaele, S., Sagner, A., Byrne, E.F., Covey, D.F., Siebold, C., Rohatgi, R., Cholesterol activates the G-protein coupled receptor smoothened to promote hedgehog signaling. eLife, 5, 2016, e20304.
-
(2016)
eLife
, vol.5
-
-
Luchetti, G.1
Sircar, R.2
Kong, J.H.3
Nachtergaele, S.4
Sagner, A.5
Byrne, E.F.6
Covey, D.F.7
Siebold, C.8
Rohatgi, R.9
-
47
-
-
85038259669
-
Multiple ligand binding sites regulate the hedgehog signal transducer Smoothened in vertebrates
-
Byrne, E.F., Luchetti, G., Rohatgi, R., Siebold, C., Multiple ligand binding sites regulate the hedgehog signal transducer Smoothened in vertebrates. Curr Opin Cell Biol 51 (2018), 81–88.
-
(2018)
Curr Opin Cell Biol
, vol.51
, pp. 81-88
-
-
Byrne, E.F.1
Luchetti, G.2
Rohatgi, R.3
Siebold, C.4
-
48
-
-
84936890311
-
Molecular dynamics simulations of GPCR–cholesterol interaction: an emerging paradigm
-
Sengupta, D., Chattopadhyay, A., Molecular dynamics simulations of GPCR–cholesterol interaction: an emerging paradigm. Biochim Biophys Acta Biomembr 1848 (2015), 1775–1782.
-
(2015)
Biochim Biophys Acta Biomembr
, vol.1848
, pp. 1775-1782
-
-
Sengupta, D.1
Chattopadhyay, A.2
-
49
-
-
84975763644
-
Interaction of G protein coupled receptors and cholesterol
-
Gimpl, G., Interaction of G protein coupled receptors and cholesterol. Chem Phys Lipids 199 (2016), 61–73.
-
(2016)
Chem Phys Lipids
, vol.199
, pp. 61-73
-
-
Gimpl, G.1
-
50
-
-
85054892021
-
Role of extracellular loops and membrane lipids for ligand recognition in the neuronal adenosine receptor type 2A: an enhanced sampling simulation study
-
Cao, R., Giorgetti, A., Bauer, A., Neumaier, B., Rossetti, G., Carloni, P., Role of extracellular loops and membrane lipids for ligand recognition in the neuronal adenosine receptor type 2A: an enhanced sampling simulation study. Molecules, 23, 2018, 2616.
-
(2018)
Molecules
, vol.23
, pp. 2616
-
-
Cao, R.1
Giorgetti, A.2
Bauer, A.3
Neumaier, B.4
Rossetti, G.5
Carloni, P.6
-
51
-
-
84983806015
-
Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region
-
Venkatakrishnan, A.J., Deupi, X., Lebon, G., Heydenreich, F.M., Flock, T., Miljus, T., Balaji, S., Bouvier, M., Veprintsev, D.B., Tate, C.G., Schertler, G.F., Diverse activation pathways in class A GPCRs converge near the G-protein-coupling region. Nature 536 (2016), 484–487.
-
(2016)
Nature
, vol.536
, pp. 484-487
-
-
Venkatakrishnan, A.J.1
Deupi, X.2
Lebon, G.3
Heydenreich, F.M.4
Flock, T.5
Miljus, T.6
Balaji, S.7
Bouvier, M.8
Veprintsev, D.B.9
Tate, C.G.10
Schertler, G.F.11
-
52
-
-
84905732337
-
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges
-
Kufareva, I., Katritch, V., Stevens, R.C., Abagyan, R., Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure 22 (2014), 1120–1139.
-
(2014)
Structure
, vol.22
, pp. 1120-1139
-
-
Kufareva, I.1
Katritch, V.2
Stevens, R.C.3
Abagyan, R.4
-
53
-
-
84939825849
-
Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models
-
Cavasotto, C.N., Palomba, D., Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun 51 (2015), 13576–13594.
-
(2015)
Chem Commun
, vol.51
, pp. 13576-13594
-
-
Cavasotto, C.N.1
Palomba, D.2
-
54
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia, C., Lesk, A.M., The relation between the divergence of sequence and structure in proteins. EMBO J 5 (1986), 823–826.
-
(1986)
EMBO J
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
55
-
-
84882741082
-
Genome-wide membrane protein structure prediction
-
Piccoli, S., Suku, E., Garonzi, M., Giorgetti, A., Genome-wide membrane protein structure prediction. Curr Genomics 14 (2013), 324–329.
-
(2013)
Curr Genomics
, vol.14
, pp. 324-329
-
-
Piccoli, S.1
Suku, E.2
Garonzi, M.3
Giorgetti, A.4
-
56
-
-
84879982797
-
Relation between sequence and structure in membrane proteins
-
Olivella, M., Gonzalez, A., Pardo, L., Deupi, X., Relation between sequence and structure in membrane proteins. Bioinformatics 29 (2013), 1589–1592.
-
(2013)
Bioinformatics
, vol.29
, pp. 1589-1592
-
-
Olivella, M.1
Gonzalez, A.2
Pardo, L.3
Deupi, X.4
-
57
-
-
77954653331
-
Structural requirements of bitter taste receptor activation
-
Brockhoff, A., Behrens, M., Niv, M.Y., Meyerhof, W., Structural requirements of bitter taste receptor activation. Proc Natl Acad Sci U S A 107 (2010), 11110–11115.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, pp. 11110-11115
-
-
Brockhoff, A.1
Behrens, M.2
Niv, M.Y.3
Meyerhof, W.4
-
58
-
-
85050119681
-
Reengineering the ligand sensitivity of the broadly tuned human bitter taste receptor TAS2R14
-
Nowak, S., Di Pizio, A., Levit, A., Niv, M.Y., Meyerhof, W., Behrens, M., Reengineering the ligand sensitivity of the broadly tuned human bitter taste receptor TAS2R14. Biochim Biophys Acta Biomembr Gen Subj 1862 (2018), 2162–2173.
-
(2018)
Biochim Biophys Acta Biomembr Gen Subj
, vol.1862
, pp. 2162-2173
-
-
Nowak, S.1
Di Pizio, A.2
Levit, A.3
Niv, M.Y.4
Meyerhof, W.5
Behrens, M.6
-
59
-
-
84973879531
-
Probing the binding pocket of the broadly tuned human bitter taste receptor TAS2R14 by chemical modification of cognate agonists
-
Karaman, R., Nowak, S., Di Pizio, A., Kitaneh, H., Abu‐ Jaish, A., Meyerhof, W., Niv, M.Y., Behrens, M., Probing the binding pocket of the broadly tuned human bitter taste receptor TAS2R14 by chemical modification of cognate agonists. Chem Biol Drug Des 88 (2016), 66–75.
-
(2016)
Chem Biol Drug Des
, vol.88
, pp. 66-75
-
-
Karaman, R.1
Nowak, S.2
Di Pizio, A.3
Kitaneh, H.4
Abu‐ Jaish, A.5
Meyerhof, W.6
Niv, M.Y.7
Behrens, M.8
-
60
-
-
85055572967
-
Bitterless guaifenesin prodrugs—design, synthesis, characterization, in vitro kinetics, and bitterness studies
-
Thawabteh, A., Lelario, F., Scrano, L., Bufo, S.A., Nowak, S., Behrens, M., Di Pizio, A., Niv, M.Y., Karaman, R., Bitterless guaifenesin prodrugs—design, synthesis, characterization, in vitro kinetics, and bitterness studies. Chem Biol Drug Des 93 (2019), 262–271.
-
(2019)
Chem Biol Drug Des
, vol.93
, pp. 262-271
-
-
Thawabteh, A.1
Lelario, F.2
Scrano, L.3
Bufo, S.A.4
Nowak, S.5
Behrens, M.6
Di Pizio, A.7
Niv, M.Y.8
Karaman, R.9
-
61
-
-
84906987340
-
Amino acid derivatives as bitter taste receptor (T2R) blockers
-
Pydi, S.P., Sobotkiewicz, T., Billakanti, R., Bhullar, R.P., Loewen, M.C., Chelikani, P., Amino acid derivatives as bitter taste receptor (T2R) blockers. J Biol Chem 289 (2014), 25054–25066.
-
(2014)
J Biol Chem
, vol.289
, pp. 25054-25066
-
-
Pydi, S.P.1
Sobotkiewicz, T.2
Billakanti, R.3
Bhullar, R.P.4
Loewen, M.C.5
Chelikani, P.6
-
62
-
-
84857483274
-
Lifting the lid on GPCRs: the role of extracellular loops
-
Wheatley, M., Wootten, D., Conner, M.T., Simms, J., Kendrick, R., Logan, R.T., Poyner, D.R., Barwell, J., Lifting the lid on GPCRs: the role of extracellular loops. Br J Pharmacol 165 (2012), 1688–1703.
-
(2012)
Br J Pharmacol
, vol.165
, pp. 1688-1703
-
-
Wheatley, M.1
Wootten, D.2
Conner, M.T.3
Simms, J.4
Kendrick, R.5
Logan, R.T.6
Poyner, D.R.7
Barwell, J.8
-
63
-
-
85008238656
-
Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family
-
Woolley, M.J., Conner, A.C., Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family. Mol Cell Endocrinol 449 (2017), 3–11.
-
(2017)
Mol Cell Endocrinol
, vol.449
, pp. 3-11
-
-
Woolley, M.J.1
Conner, A.C.2
-
64
-
-
64749106745
-
Systematic multiscale simulation of membrane protein systems
-
Ayton, G.S., Voth, G.A., Systematic multiscale simulation of membrane protein systems. Curr Opin Struct Biol 19 (2009), 138–144.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 138-144
-
-
Ayton, G.S.1
Voth, G.A.2
-
65
-
-
85062344382
-
Coarse-grained molecular dynamics simulations of membrane proteins
-
M.S.P. Sansom P.C. Biggin RSC Publishing
-
Rouse, S., Carpenter, T., Sansom, M.S., Coarse-grained molecular dynamics simulations of membrane proteins. Sansom, M.S.P., Biggin, P.C., (eds.) Molecular Simulations and Biomembranes: From Biophysics to Function, vol 20, 2010, RSC Publishing, 56–75.
-
(2010)
Molecular Simulations and Biomembranes: From Biophysics to Function
, vol.20
, pp. 56-75
-
-
Rouse, S.1
Carpenter, T.2
Sansom, M.S.3
-
66
-
-
84867684737
-
Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes
-
Leguèbe, M., Nguyen, C., Capece, L., Hoang, Z., Giorgetti, A., Carloni, P., Hybrid molecular mechanics/coarse-grained simulations for structural prediction of G-protein coupled receptor/ligand complexes. PLoS One, 7, 2012, e47332.
-
(2012)
PLoS One
, vol.7
-
-
Leguèbe, M.1
Nguyen, C.2
Capece, L.3
Hoang, Z.4
Giorgetti, A.5
Carloni, P.6
-
67
-
-
85042027176
-
Predicting ligand binding poses for low-resolution membrane protein models: perspectives from multiscale simulations
-
Schneider, J., Korshunova, K., Musiani, F., Alfonso-Prieto, M., Giorgetti, A., Carloni, P., Predicting ligand binding poses for low-resolution membrane protein models: perspectives from multiscale simulations. Biochem Biophys Res Commun 498 (2018), 366–374.
-
(2018)
Biochem Biophys Res Commun
, vol.498
, pp. 366-374
-
-
Schneider, J.1
Korshunova, K.2
Musiani, F.3
Alfonso-Prieto, M.4
Giorgetti, A.5
Carloni, P.6
-
68
-
-
84878530705
-
Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding
-
Marchiori, A., Capece, L., Giorgetti, A., Gasparini, P., Behrens, M., Carloni, P., Meyerhof, W., Coarse-grained/molecular mechanics of the TAS2R38 bitter taste receptor: experimentally-validated detailed structural prediction of agonist binding. PLoS One, 8, 2013, e64675.
-
(2013)
PLoS One
, vol.8
-
-
Marchiori, A.1
Capece, L.2
Giorgetti, A.3
Gasparini, P.4
Behrens, M.5
Carloni, P.6
Meyerhof, W.7
-
69
-
-
80052001378
-
Pathway and mechanism of drug binding to G-protein-coupled receptors
-
Dror, R.O., Pan, A.C., Arlow, D.H., Borhani, D.W., Maragakis, P., Shan, Y., Xu, H., Shaw, D.E., Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci U S A 108 (2011), 13118–13123.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 13118-13123
-
-
Dror, R.O.1
Pan, A.C.2
Arlow, D.H.3
Borhani, D.W.4
Maragakis, P.5
Shan, Y.6
Xu, H.7
Shaw, D.E.8
-
70
-
-
84863115467
-
Structure and dynamics of the M3 muscarinic acetylcholine receptor
-
Kruse, A.C., Hu, J., Pan, A.C., Arlow, D.H., Rosenbaum, D.M., Rosemond, E., Green, H.F., Liu, T., Chae, P.S., Dror, R.O., Shaw, D.E., Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature 482 (2012), 552–556.
-
(2012)
Nature
, vol.482
, pp. 552-556
-
-
Kruse, A.C.1
Hu, J.2
Pan, A.C.3
Arlow, D.H.4
Rosenbaum, D.M.5
Rosemond, E.6
Green, H.F.7
Liu, T.8
Chae, P.S.9
Dror, R.O.10
Shaw, D.E.11
-
71
-
-
84887620421
-
Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
-
Dror, R.O., Green, H.F., Valant, C., Borhani, D.W., Valcourt, J.R., Pan, A.C., Arlow, D.H., Canals, M., Lane, J.R., Rahmani, R., Baell, J.B., Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature 503 (2013), 295–299.
-
(2013)
Nature
, vol.503
, pp. 295-299
-
-
Dror, R.O.1
Green, H.F.2
Valant, C.3
Borhani, D.W.4
Valcourt, J.R.5
Pan, A.C.6
Arlow, D.H.7
Canals, M.8
Lane, J.R.9
Rahmani, R.10
Baell, J.B.11
-
72
-
-
84864221004
-
A new era of GPCR structural and chemical biology
-
Granier, S., Kobilka, B., A new era of GPCR structural and chemical biology. Nat Chem Biol 8 (2012), 670–673.
-
(2012)
Nat Chem Biol
, vol.8
, pp. 670-673
-
-
Granier, S.1
Kobilka, B.2
-
73
-
-
85040789290
-
Vertebrate bitter taste receptors: keys for survival in changing environments
-
Behrens, M., Meyerhof, W., Vertebrate bitter taste receptors: keys for survival in changing environments. J Agric Food Chem 66 (2016), 2204–2213.
-
(2016)
J Agric Food Chem
, vol.66
, pp. 2204-2213
-
-
Behrens, M.1
Meyerhof, W.2
-
74
-
-
85021857088
-
GPCR dynamics: structures in motion
-
Latorraca, N.R., Venkatakrishnan, A.J., Dror, R.O., GPCR dynamics: structures in motion. Chem Rev 117 (2016), 139–155.
-
(2016)
Chem Rev
, vol.117
, pp. 139-155
-
-
Latorraca, N.R.1
Venkatakrishnan, A.J.2
Dror, R.O.3
-
75
-
-
84975518316
-
G-protein coupled receptors: advances in simulation and drug discovery
-
Miao, Y., McCammon, J.A., G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol 41 (2016), 83–89.
-
(2016)
Curr Opin Struct Biol
, vol.41
, pp. 83-89
-
-
Miao, Y.1
McCammon, J.A.2
-
76
-
-
85036642088
-
GPCRs: what can we learn from molecular dynamics simulations?
-
Velgy, N., Hedger, G., Biggin, P.C., GPCRs: what can we learn from molecular dynamics simulations?. Methods Mol Biol 1705 (2018), 133–158.
-
(2018)
Methods Mol Biol
, vol.1705
, pp. 133-158
-
-
Velgy, N.1
Hedger, G.2
Biggin, P.C.3
-
77
-
-
85036629321
-
Investigating small-molecule ligand binding to G protein-coupled receptors with biased or unbiased molecular dynamics simulations
-
Marino, K.A., Filizola, M., Investigating small-molecule ligand binding to G protein-coupled receptors with biased or unbiased molecular dynamics simulations. Methods Mol Biol 1705 (2018), 351–364.
-
(2018)
Methods Mol Biol
, vol.1705
, pp. 351-364
-
-
Marino, K.A.1
Filizola, M.2
-
78
-
-
85058454913
-
An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber
-
Meral, D., Provasi, D., Filizola, M., An efficient strategy to estimate thermodynamics and kinetics of G protein-coupled receptor activation using metadynamics and maximum caliber. J Chem Phys, 149, 2018, 224101.
-
(2018)
J Chem Phys
, vol.149
-
-
Meral, D.1
Provasi, D.2
Filizola, M.3
-
79
-
-
85016114203
-
Interplay of G protein-coupled receptors with the membrane: insights from supra-atomic coarse grain molecular dynamics simulations
-
Periole, X., Interplay of G protein-coupled receptors with the membrane: insights from supra-atomic coarse grain molecular dynamics simulations. Chem Rev 117 (2017), 156–185.
-
(2017)
Chem Rev
, vol.117
, pp. 156-185
-
-
Periole, X.1
-
80
-
-
85047212092
-
Structural basis of smoothened activation in hedgehog signaling
-
Huang, P., Zheng, S., Wierbowski, B.M., Kim, Y., Nedelcu, D., Aravena, L., Liu, J., Kruse, A.C., Salic, A., Structural basis of smoothened activation in hedgehog signaling. Cell 174 (2018), 312–324.
-
(2018)
Cell
, vol.174
, pp. 312-324
-
-
Huang, P.1
Zheng, S.2
Wierbowski, B.M.3
Kim, Y.4
Nedelcu, D.5
Aravena, L.6
Liu, J.7
Kruse, A.C.8
Salic, A.9
-
81
-
-
85050176202
-
Carpenter B: PtdIns (4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling
-
Yen, H.Y., Hoi, K.K., Liko, I., Hedger, G., Horrell, M.R., Song, W., Wu, D., Heine, P., Warne, T., Lee, Y., Carpenter B: PtdIns (4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling. Nature 559 (2018), 423–427.
-
(2018)
Nature
, vol.559
, pp. 423-427
-
-
Yen, H.Y.1
Hoi, K.K.2
Liko, I.3
Hedger, G.4
Horrell, M.R.5
Song, W.6
Wu, D.7
Heine, P.8
Warne, T.9
Lee, Y.10
|