메뉴 건너뛰기




Volumn 498, Issue 2, 2018, Pages 366-374

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations

Author keywords

Bitter taste receptor; Chemosensory receptor; G protein coupled receptor; Homology modeling; Molecular docking; Molecular mechanics coarse grained simulations

Indexed keywords

G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; LIGAND;

EID: 85042027176     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2018.01.160     Document Type: Article
Times cited : (29)

References (145)
  • 1
    • 70350038016 scopus 로고    scopus 로고
    • Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin
    • Almén, M.S., Nordström, K.J., Fredriksson, R., Schiöth, H.B., Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol., 7, 2009, 50.
    • (2009) BMC Biol. , vol.7 , pp. 50
    • Almén, M.S.1    Nordström, K.J.2    Fredriksson, R.3    Schiöth, H.B.4
  • 2
    • 84882741082 scopus 로고    scopus 로고
    • Genome-wide membrane protein structure prediction
    • Piccoli, S., Suku, E., Garonzi, M., Giorgetti, A., Genome-wide membrane protein structure prediction. Curr. Genom. 14 (2013), 324–329.
    • (2013) Curr. Genom. , vol.14 , pp. 324-329
    • Piccoli, S.1    Suku, E.2    Garonzi, M.3    Giorgetti, A.4
  • 5
    • 84894152157 scopus 로고    scopus 로고
    • Current and emerging opportunities for molecular simulations in structure-based drug design
    • Michel, J., Current and emerging opportunities for molecular simulations in structure-based drug design. Phys. Chem. Chem. Phys. 16 (2014), 4465–4477.
    • (2014) Phys. Chem. Chem. Phys. , vol.16 , pp. 4465-4477
    • Michel, J.1
  • 7
    • 84930252131 scopus 로고    scopus 로고
    • Protein Modeling and Structure-based Drug Design, Drug Design
    • Springer Berlin Heidelberg
    • Klebe, G., Protein Modeling and Structure-based Drug Design, Drug Design. 2013, Springer Berlin Heidelberg, 429–448.
    • (2013) , pp. 429-448
    • Klebe, G.1
  • 8
    • 84876469966 scopus 로고    scopus 로고
    • Emerging topics in structure-based virtual screening
    • Rastelli, G., Emerging topics in structure-based virtual screening. Pharm. Res. 30 (2013), 1458–1463.
    • (2013) Pharm. Res. , vol.30 , pp. 1458-1463
    • Rastelli, G.1
  • 11
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • Kufareva, I., Rueda, M., Katritch, V., Dock, G., Stevens, R.C., Abagyan, R., Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 19 (2011), 1108–1126.
    • (2011) Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Dock, G.4    Stevens, R.C.5    Abagyan, R.6
  • 12
    • 84905732337 scopus 로고    scopus 로고
    • 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
  • 13
    • 84871539979 scopus 로고    scopus 로고
    • Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines
    • Beuming, T., Sherman, W., Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines. J. Chem. Inf. Model. 52 (2012), 3263–3277.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 3263-3277
    • Beuming, T.1    Sherman, W.2
  • 14
    • 0022706389 scopus 로고
    • 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.
    • (1986) EMBO J. , vol.5 , pp. 823
    • Chothia, C.1    Lesk, A.M.2
  • 15
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker, D., Sali, A., Protein structure prediction and structural genomics. Science 294 (2001), 93–96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 16
    • 41149132407 scopus 로고    scopus 로고
    • Comparative Protein Structure Modeling Using MODELLER, Current Protocols in Protein Science
    • John Wiley & Sons, Inc
    • Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.-y., Pieper, U., Sali, A., Comparative Protein Structure Modeling Using MODELLER, Current Protocols in Protein Science. 2007, John Wiley & Sons, Inc, 2.9.1–2.9.31.
    • (2007) , pp. 2.9.1-2.9.31
    • Eswar, N.1    Webb, B.2    Marti-Renom, M.A.3    Madhusudhan, M.S.4    Eramian, D.5    Shen, M.-Y.6    Pieper, U.7    Sali, A.8
  • 17
    • 84879982797 scopus 로고    scopus 로고
    • 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
  • 18
    • 21644437700 scopus 로고    scopus 로고
    • Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets
    • Camacho, C.J., Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets. Proteins 60 (2005), 245–251.
    • (2005) Proteins , vol.60 , pp. 245-251
    • Camacho, C.J.1
  • 19
    • 66649096395 scopus 로고    scopus 로고
    • Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors
    • Angel, T.E., Chance, M.R., Palczewski, K., Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors. Proc. Natl. Acad. Sci. USA 106 (2009), 8555–8560.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 8555-8560
    • Angel, T.E.1    Chance, M.R.2    Palczewski, K.3
  • 20
    • 77953488648 scopus 로고    scopus 로고
    • Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation
    • Nygaard, R., Valentin-Hansen, L., Mokrosinski, J., Frimurer, T.M., Schwartz, T.W., Conserved water-mediated hydrogen bond network between TM-I, -II, -VI, and -VII in 7TM receptor activation. J. Biol. Chem. 285 (2010), 19625–19636.
    • (2010) J. Biol. Chem. , vol.285 , pp. 19625-19636
    • Nygaard, R.1    Valentin-Hansen, L.2    Mokrosinski, J.3    Frimurer, T.M.4    Schwartz, T.W.5
  • 21
    • 80054950510 scopus 로고    scopus 로고
    • Molecular dynamics simulations and drug discovery
    • Durrant, J.D., McCammon, J.A., Molecular dynamics simulations and drug discovery. BMC Biol., 9, 2011, 71.
    • (2011) BMC Biol. , vol.9 , pp. 71
    • Durrant, J.D.1    McCammon, J.A.2
  • 22
    • 84939825849 scopus 로고    scopus 로고
    • 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
  • 28
    • 85029011074 scopus 로고    scopus 로고
    • Drug discovery and molecular dynamics: methods, applications and perspective beyond the second timescale
    • Martínez-Rosell, G., Giorgino, T., Harvey, M., de Fabritiis, G., Drug discovery and molecular dynamics: methods, applications and perspective beyond the second timescale. Curr. Top. Med. Chem. 17 (2017), 2617–2625.
    • (2017) Curr. Top. Med. Chem. , vol.17 , pp. 2617-2625
    • Martínez-Rosell, G.1    Giorgino, T.2    Harvey, M.3    de Fabritiis, G.4
  • 29
    • 84969122144 scopus 로고    scopus 로고
    • Role of molecular dynamics and related methods in drug discovery
    • De Vivo, M., Masetti, M., Bottegoni, G., Cavalli, A., Role of molecular dynamics and related methods in drug discovery. J. Med. Chem. 59 (2016), 4035–4061.
    • (2016) J. Med. Chem. , vol.59 , pp. 4035-4061
    • De Vivo, M.1    Masetti, M.2    Bottegoni, G.3    Cavalli, A.4
  • 30
    • 85036629321 scopus 로고    scopus 로고
    • Investigating Small-molecule Ligand Binding to G Protein-coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations, Computational Methods for GPCR Drug Discovery
    • Springer
    • Marino, K.A., Filizola, M., Investigating Small-molecule Ligand Binding to G Protein-coupled Receptors with Biased or Unbiased Molecular Dynamics Simulations, Computational Methods for GPCR Drug Discovery. 2018, Springer, 351–364.
    • (2018) , pp. 351-364
    • Marino, K.A.1    Filizola, M.2
  • 31
    • 84896691815 scopus 로고    scopus 로고
    • Extrasensory perception: odorant and taste receptors beyond the nose and mouth
    • Foster, S.R., Roura, E., Thomas, W.G., Extrasensory perception: odorant and taste receptors beyond the nose and mouth. Pharmacol. Ther. 142 (2014), 41–61.
    • (2014) Pharmacol. Ther. , vol.142 , pp. 41-61
    • Foster, S.R.1    Roura, E.2    Thomas, W.G.3
  • 32
  • 33
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M.M., Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77 (1996), 1905–1908.
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 34
    • 0020488742 scopus 로고
    • Collective variable description of small-amplitude conformational fluctuations in a globular protein
    • Noguti, T., Gō, N., Collective variable description of small-amplitude conformational fluctuations in a globular protein. Nature 296 (1982), 776–778.
    • (1982) Nature , vol.296 , pp. 776-778
    • Noguti, T.1    Gō, N.2
  • 36
    • 85030656509 scopus 로고    scopus 로고
    • Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes
    • in press
    • Brandner, A., Schüller, A., Melo, F., Pantano, S., Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes. BBRC (Biochem. Biophys. Res. Commun.), 2017, 10.1016/j.bbrc.2017.09.086 in press.
    • (2017) BBRC (Biochem. Biophys. Res. Commun.)
    • Brandner, A.1    Schüller, A.2    Melo, F.3    Pantano, S.4
  • 38
    • 84934435433 scopus 로고    scopus 로고
    • The Martini Coarse-grained Force Field, Methods Mol. Biol
    • Humana Press
    • Periole, X., Marrink, S.-J., The Martini Coarse-grained Force Field, Methods Mol. Biol. 2012, Humana Press, 533–565.
    • (2012) , pp. 533-565
    • Periole, X.1    Marrink, S.-J.2
  • 41
    • 29944444169 scopus 로고    scopus 로고
    • Implicit solvent simulation models for biomembranes
    • Brannigan, G., Lin, L.C.L., Brown, F.L.H., Implicit solvent simulation models for biomembranes. Eur. Biophys. J. 35 (2005), 104–124.
    • (2005) Eur. Biophys. J. , vol.35 , pp. 104-124
    • Brannigan, G.1    Lin, L.C.L.2    Brown, F.L.H.3
  • 43
    • 17044393884 scopus 로고    scopus 로고
    • Coarse-grained models for proteins
    • Tozzini, V., Coarse-grained models for proteins. Curr. Opin. Struct. Biol. 15 (2005), 144–150.
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 144-150
    • Tozzini, V.1
  • 44
    • 33748448490 scopus 로고    scopus 로고
    • A natural coarse graining for simulating large biomolecular motion
    • Gohlke, H., Thorpe, M.F., A natural coarse graining for simulating large biomolecular motion. Biophys. J. 91 (2006), 2115–2120.
    • (2006) Biophys. J. , vol.91 , pp. 2115-2120
    • Gohlke, H.1    Thorpe, M.F.2
  • 45
    • 20444377701 scopus 로고    scopus 로고
    • Electrostatic mechanism of nucleosomal array folding revealed by computer simulation
    • Sun, J., Zhang, Q., Schlick, T., Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc. Natl. Acad. Sci. USA 102 (2005), 8180–8185.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 8180-8185
    • Sun, J.1    Zhang, Q.2    Schlick, T.3
  • 46
    • 77952355398 scopus 로고    scopus 로고
    • A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics
    • Dans, P.D., Zeida, A., Machado, M.a.R., Pantano, S., A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics. J. Chem. Theor. Comput. 6 (2010), 1711–1725.
    • (2010) J. Chem. Theor. Comput. , vol.6 , pp. 1711-1725
    • Dans, P.D.1    Zeida, A.2    Machado, M.A.R.3    Pantano, S.4
  • 47
    • 84893060375 scopus 로고    scopus 로고
    • Computer Simulation of Self-assembling Macromolecules, Hierarchical Macromolecular Structures: 60 Years after the Staudinger Nobel Prize II
    • Springer
    • Fiorin, G., Klein, M.L., DeVane, R., Shinoda, W., Computer Simulation of Self-assembling Macromolecules, Hierarchical Macromolecular Structures: 60 Years after the Staudinger Nobel Prize II. 2013, Springer, 93–107.
    • (2013) , pp. 93-107
    • Fiorin, G.1    Klein, M.L.2    DeVane, R.3    Shinoda, W.4
  • 49
    • 77951212412 scopus 로고    scopus 로고
    • PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
    • Gopal, S.M., Mukherjee, S., Cheng, Y.M., Feig, M., PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy. Proteins 78 (2010), 1266–1281.
    • (2010) Proteins , vol.78 , pp. 1266-1281
    • Gopal, S.M.1    Mukherjee, S.2    Cheng, Y.M.3    Feig, M.4
  • 51
    • 84975505079 scopus 로고    scopus 로고
    • Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale
    • Chavent, M., Duncan, A.L., Sansom, M.S., Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale. Curr. Opin. Struct. Biol. 40 (2016), 8–16.
    • (2016) Curr. Opin. Struct. Biol. , vol.40 , pp. 8-16
    • Chavent, M.1    Duncan, A.L.2    Sansom, M.S.3
  • 52
    • 39449131104 scopus 로고    scopus 로고
    • Coarse-grained simulation: a high-throughput computational approach to membrane proteins
    • Sansom, M.S., Scott, K.A., Bond, P.J., Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem. Soc. Trans. 36 (2008), 27–32.
    • (2008) Biochem. Soc. Trans. , vol.36 , pp. 27-32
    • Sansom, M.S.1    Scott, K.A.2    Bond, P.J.3
  • 53
    • 85019360382 scopus 로고    scopus 로고
    • Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models
    • Liao, C., Zhao, X., Liu, J., Schneebeli, S.T., Shelley, J.C., Li, J., Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models. Phys. Chem. Chem. Phys. 19 (2017), 9181–9188.
    • (2017) Phys. Chem. Chem. Phys. , vol.19 , pp. 9181-9188
    • Liao, C.1    Zhao, X.2    Liu, J.3    Schneebeli, S.T.4    Shelley, J.C.5    Li, J.6
  • 54
    • 34548146523 scopus 로고    scopus 로고
    • G protein-coupled receptors self-assemble in dynamics simulations of model bilayers
    • Periole, X., Huber, T., Marrink, S.-J., Sakmar, T.P., G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J. Am. Chem. Soc. 129 (2007), 10126–10132.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 10126-10132
    • Periole, X.1    Huber, T.2    Marrink, S.-J.3    Sakmar, T.P.4
  • 55
    • 27944495588 scopus 로고    scopus 로고
    • Multiscale modeling of lipids and lipid bilayers
    • Lyubartsev, A.P., Multiscale modeling of lipids and lipid bilayers. Eur. Biophys. J. 35 (2005), 53–61.
    • (2005) Eur. Biophys. J. , vol.35 , pp. 53-61
    • Lyubartsev, A.P.1
  • 56
    • 14544291957 scopus 로고    scopus 로고
    • A multiscale coarse-graining method for biomolecular systems
    • Izvekov, S., Voth, G.A., A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B 109 (2005), 2469–2473.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 2469-2473
    • Izvekov, S.1    Voth, G.A.2
  • 57
    • 33748266722 scopus 로고    scopus 로고
    • Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound Ion Channel
    • Shi, Q., Izvekov, S., Voth, G.A., Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound Ion Channel. J. Phys. Chem. B 110 (2006), 15045–15048.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 15045-15048
    • Shi, Q.1    Izvekov, S.2    Voth, G.A.3
  • 58
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • Ayton, G.S., Noid, W.G., Voth, G.A., Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 17 (2007), 192–198.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 192-198
    • Ayton, G.S.1    Noid, W.G.2    Voth, G.A.3
  • 59
    • 21744452297 scopus 로고    scopus 로고
    • Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations
    • Ding, F., Guo, W., Dokholyan, N.V., Shakhnovich, E.I., Shea, J.-E., Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations. J. Mol. Biol. 350 (2005), 1035–1050.
    • (2005) J. Mol. Biol. , vol.350 , pp. 1035-1050
    • Ding, F.1    Guo, W.2    Dokholyan, N.V.3    Shakhnovich, E.I.4    Shea, J.-E.5
  • 60
    • 33646123091 scopus 로고    scopus 로고
    • Coarse-grained modeling of the actin filament derived from atomistic-scale simulations
    • Chu, J.-W., Voth, G.A., Coarse-grained modeling of the actin filament derived from atomistic-scale simulations. Biophys. J. 90 (2006), 1572–1582.
    • (2006) Biophys. J. , vol.90 , pp. 1572-1582
    • Chu, J.-W.1    Voth, G.A.2
  • 62
    • 18744391399 scopus 로고    scopus 로고
    • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    • Villa, E., Balaeff, A., Schulten, K., Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc. Natl. Acad. Sci. USA 102 (2005), 6783–6788.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3
  • 64
    • 80053475897 scopus 로고    scopus 로고
    • A hybrid all-atom/coarse grain model for multiscale simulations of DNA
    • Machado, M.R., Dans, P.D., Pantano, S., A hybrid all-atom/coarse grain model for multiscale simulations of DNA. Phys. Chem. Chem. Phys. 13 (2011), 18134–18144.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 18134-18144
    • Machado, M.R.1    Dans, P.D.2    Pantano, S.3
  • 65
    • 33748250745 scopus 로고    scopus 로고
    • Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers
    • Izvekov, S., Voth, G.A., Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theor. Comput. 2 (2006), 637–648.
    • (2006) J. Chem. Theor. Comput. , vol.2 , pp. 637-648
    • Izvekov, S.1    Voth, G.A.2
  • 66
    • 84907994630 scopus 로고    scopus 로고
    • Direct mixing of atomistic solutes and coarse-grained water
    • Orsi, M., Ding, W., Palaiokostas, M., Direct mixing of atomistic solutes and coarse-grained water. J. Chem. Theor. Comput. 10 (2014), 4684–4693.
    • (2014) J. Chem. Theor. Comput. , vol.10 , pp. 4684-4693
    • Orsi, M.1    Ding, W.2    Palaiokostas, M.3
  • 67
    • 83455255623 scopus 로고    scopus 로고
    • The ELBA force field for coarse-grain modeling of lipid membranes
    • Orsi, M., Essex, J.W., The ELBA force field for coarse-grain modeling of lipid membranes. PLoS One, 6, 2011, e28637.
    • (2011) PLoS One , vol.6
    • Orsi, M.1    Essex, J.W.2
  • 68
    • 84944231550 scopus 로고    scopus 로고
    • A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes
    • Genheden, S., Essex, J.W., A simple and transferable all-atom/coarse-grained hybrid model to study membrane processes. J. Chem. Theor. Comput. 11 (2015), 4749–4759.
    • (2015) J. Chem. Theor. Comput. , vol.11 , pp. 4749-4759
    • Genheden, S.1    Essex, J.W.2
  • 69
    • 79959749835 scopus 로고    scopus 로고
    • Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites
    • Rzepiela, A.J., Louhivuori, M., Peter, C., Marrink, S.J., Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites. Phys. Chem. Chem. Phys., 13, 2011, 10437.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 10437
    • Rzepiela, A.J.1    Louhivuori, M.2    Peter, C.3    Marrink, S.J.4
  • 70
    • 84875777145 scopus 로고    scopus 로고
    • Mixing MARTINI: electrostatic coupling in hybrid atomistic–coarse-grained biomolecular simulations
    • Wassenaar, T.A., Ingólfsson, H.I., Prieß, M., Marrink, S.J., Schäfer, L.V., Mixing MARTINI: electrostatic coupling in hybrid atomistic–coarse-grained biomolecular simulations. J. Phys. Chem. B 117 (2013), 3516–3530.
    • (2013) J. Phys. Chem. B , vol.117 , pp. 3516-3530
    • Wassenaar, T.A.1    Ingólfsson, H.I.2    Prieß, M.3    Marrink, S.J.4    Schäfer, L.V.5
  • 71
    • 84869023641 scopus 로고    scopus 로고
    • Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged side chains
    • Han, W., Schulten, K., Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: improved backbone hydration and interactions between charged side chains. J. Chem. Theor. Comput. 8 (2012), 4413–4424.
    • (2012) J. Chem. Theor. Comput. , vol.8 , pp. 4413-4424
    • Han, W.1    Schulten, K.2
  • 72
    • 84862929076 scopus 로고    scopus 로고
    • Parameterization of PACE force field for membrane environment and simulation of helical peptides and helix–helix association
    • Wan, C.-K., Han, W., Wu, Y.-D., Parameterization of PACE force field for membrane environment and simulation of helical peptides and helix–helix association. J. Chem. Theor. Comput. 8 (2011), 300–313.
    • (2011) J. Chem. Theor. Comput. , vol.8 , pp. 300-313
    • Wan, C.-K.1    Han, W.2    Wu, Y.-D.3
  • 73
    • 85010781152 scopus 로고    scopus 로고
    • Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides
    • Ward, M.D., Nangia, S., May, E.R., Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides. J. Comput. Chem. 38 (2017), 1462–1471.
    • (2017) J. Comput. Chem. , vol.38 , pp. 1462-1471
    • Ward, M.D.1    Nangia, S.2    May, E.R.3
  • 74
    • 28844494903 scopus 로고    scopus 로고
    • Coarse-grained model of proteins incorporating atomistic detail of the active site
    • Neri, M., Anselmi, C., Cascella, M., Maritan, A., Carloni, P., Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett., 95, 2005.
    • (2005) Phys. Rev. Lett. , vol.95
    • Neri, M.1    Anselmi, C.2    Cascella, M.3    Maritan, A.4    Carloni, P.5
  • 76
    • 84867684737 scopus 로고    scopus 로고
    • 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
  • 77
    • 85034213592 scopus 로고    scopus 로고
    • Hybrid all-atom/coarse-grained simulations of proteins by direct coupling of CHARMM and PRIMO force fields
    • Kar, P., Feig, M., Hybrid all-atom/coarse-grained simulations of proteins by direct coupling of CHARMM and PRIMO force fields. J. Chem. Theor. Comput. 13 (2017), 5753–5765.
    • (2017) J. Chem. Theor. Comput. , vol.13 , pp. 5753-5765
    • Kar, P.1    Feig, M.2
  • 78
    • 33748667337 scopus 로고    scopus 로고
    • Soft sticky dipole potential for liquid water: a new model
    • Liu, Y., Ichiye, T., Soft sticky dipole potential for liquid water: a new model. J. Phys. Chem. 100 (1996), 2723–2730.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2723-2730
    • Liu, Y.1    Ichiye, T.2
  • 79
    • 6744234112 scopus 로고
    • Modification of the overlap potential to mimic a linear site–site potential
    • Gay, J., Berne, B., Modification of the overlap potential to mimic a linear site–site potential. J. Chem. Phys. 74 (1981), 3316–3319.
    • (1981) J. Chem. Phys. , vol.74 , pp. 3316-3319
    • Gay, J.1    Berne, B.2
  • 81
    • 77950568789 scopus 로고    scopus 로고
    • Coarse-grain modelling of DMPC and DOPC lipid bilayers
    • Orsi, M., Michel, J., Essex, J.W., Coarse-grain modelling of DMPC and DOPC lipid bilayers. J. Phys. Condens. Matter, 22, 2010, 155106.
    • (2010) J. Phys. Condens. Matter , vol.22 , pp. 155106
    • Orsi, M.1    Michel, J.2    Essex, J.W.3
  • 82
    • 0006161383 scopus 로고    scopus 로고
    • On the choice of dihedral angle potential energy functions for n-alkanes
    • Schuler, L.D., Van Gunsteren, W.F., On the choice of dihedral angle potential energy functions for n-alkanes. Mol. Simulat. 25 (2000), 301–319.
    • (2000) Mol. Simulat. , vol.25 , pp. 301-319
    • Schuler, L.D.1    Van Gunsteren, W.F.2
  • 83
    • 0035425883 scopus 로고    scopus 로고
    • An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase
    • Schuler, L.D., Daura, X., Van Gunsteren, W.F., An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase. J. Comput. Chem. 22 (2001), 1205–1218.
    • (2001) J. Comput. Chem. , vol.22 , pp. 1205-1218
    • Schuler, L.D.1    Daura, X.2    Van Gunsteren, W.F.3
  • 84
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C., Villa, A., Mark, A.E., Van Gunsteren, W.F., A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25 (2004), 1656–1676.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 86
    • 0019569599 scopus 로고
    • Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation
    • Gō, N., Abe, H., Noninteracting local-structure model of folding and unfolding transition in globular proteins. I. Formulation. Biopolymers 20 (1981), 991–1011.
    • (1981) Biopolymers , vol.20 , pp. 991-1011
    • Gō, N.1    Abe, H.2
  • 88
    • 84906249784 scopus 로고    scopus 로고
    • Transferring the primo coarse-grained force field to the membrane environment: simulations of membrane proteins and helix–helix association
    • Kar, P., Gopal, S.M., Cheng, Y.-M., Panahi, A., Feig, M., Transferring the primo coarse-grained force field to the membrane environment: simulations of membrane proteins and helix–helix association. J. Chem. Theor. Comput. 10 (2014), 3459–3472.
    • (2014) J. Chem. Theor. Comput. , vol.10 , pp. 3459-3472
    • Kar, P.1    Gopal, S.M.2    Cheng, Y.-M.3    Panahi, A.4    Feig, M.5
  • 89
    • 17444426051 scopus 로고    scopus 로고
    • A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes
    • Tanizaki, S., Feig, M., A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes. J. Chem. Phys., 122, 2005, 124706.
    • (2005) J. Chem. Phys. , vol.122 , pp. 124706
    • Tanizaki, S.1    Feig, M.2
  • 90
    • 84923358082 scopus 로고    scopus 로고
    • Interactions of amino acid side-chain analogs within membrane environments
    • Mirjalili, V., Feig, M., Interactions of amino acid side-chain analogs within membrane environments. J. Phys. Chem. B 119 (2015), 2877–2885.
    • (2015) J. Phys. Chem. B , vol.119 , pp. 2877-2885
    • Mirjalili, V.1    Feig, M.2
  • 93
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • B. Pullman Springer Dordrecht
    • Berendsen, H.J., Postma, J.P., van Gunsteren, W.F., Hermans, J., Interaction models for water in relation to protein hydration. Pullman, B., (eds.) Intermolecular Forces, 1981, Springer, Dordrecht, 331–342.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.1    Postma, J.P.2    van Gunsteren, W.F.3    Hermans, J.4
  • 94
    • 44749084234 scopus 로고
    • Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations
    • Osher, S., Sethian, J.A., Fronts propagating with curvature-dependent speed: algorithms based on Hamilton-Jacobi formulations. J. Comput. Phys. 79 (1988), 12–49.
    • (1988) J. Comput. Phys. , vol.79 , pp. 12-49
    • Osher, S.1    Sethian, J.A.2
  • 95
  • 96
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl, E., Hess, B., van der Spoel, D., GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001), 306–317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 98
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess, B., Kutzner, C., van der Spoel, D., Lindahl, E., GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theor. Comput. 4 (2008), 435–447.
    • (2008) J. Chem. Theor. Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    van der Spoel, D.3    Lindahl, E.4
  • 102
    • 0028338534 scopus 로고
    • GCRDb: a G-protein-coupled receptor database
    • Kolakowski, L.F. Jr., GCRDb: a G-protein-coupled receptor database. Recept. Channel 2 (1994), 1–7.
    • (1994) Recept. Channel , vol.2 , pp. 1-7
    • Kolakowski, L.F.1
  • 103
    • 0038024615 scopus 로고    scopus 로고
    • 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
  • 112
    • 15644369847 scopus 로고    scopus 로고
    • Design, synthesis, and pharmacological characterization of (+)-2-aminobicyclo [3.1. 0] hexane-2, 6-dicarboxylic acid (LY354740): a potent, selective, and orally active group 2 metabotropic glutamate receptor agonist possessing anticonvulsant and anxiolytic properties
    • Monn, J.A., Valli, M.J., Massey, S.M., Wright, R.A., Salhoff, C.R., Johnson, B.G., Howe, T., Alt, C.A., Rhodes, G.A., Robey, R.L., Design, synthesis, and pharmacological characterization of (+)-2-aminobicyclo [3.1. 0] hexane-2, 6-dicarboxylic acid (LY354740): a potent, selective, and orally active group 2 metabotropic glutamate receptor agonist possessing anticonvulsant and anxiolytic properties. J. Med. Chem. 40 (1997), 528–537.
    • (1997) J. Med. Chem. , vol.40 , pp. 528-537
    • Monn, J.A.1    Valli, M.J.2    Massey, S.M.3    Wright, R.A.4    Salhoff, C.R.5    Johnson, B.G.6    Howe, T.7    Alt, C.A.8    Rhodes, G.A.9    Robey, R.L.10
  • 113
    • 85007099137 scopus 로고    scopus 로고
    • Discovery of (1 S, 2 R, 3 S, 4 S, 5 R, 6 R)-2-Amino-3-[(3, 4-difluorophenyl) sulfanylmethyl]-4-hydroxy-bicyclo [3.1. 0] hexane-2, 6-dicarboxylic acid hydrochloride (LY3020371· HCl): a potent, metabotropic glutamate 2/3 receptor antagonist with antidepressant-like activity
    • Chappell, M.D., Li, R., Smith, S.C., Dressman, B.A., Tromiczak, E.G., Tripp, A.E., Blanco, M.-J., Vetman, T., Quimby, S.J., Matt, J., Discovery of (1 S, 2 R, 3 S, 4 S, 5 R, 6 R)-2-Amino-3-[(3, 4-difluorophenyl) sulfanylmethyl]-4-hydroxy-bicyclo [3.1. 0] hexane-2, 6-dicarboxylic acid hydrochloride (LY3020371· HCl): a potent, metabotropic glutamate 2/3 receptor antagonist with antidepressant-like activity. J. Med. Chem. 59 (2016), 10974–10993.
    • (2016) J. Med. Chem. , vol.59 , pp. 10974-10993
    • Chappell, M.D.1    Li, R.2    Smith, S.C.3    Dressman, B.A.4    Tromiczak, E.G.5    Tripp, A.E.6    Blanco, M.-J.7    Vetman, T.8    Quimby, S.J.9    Matt, J.10
  • 114
    • 84918801398 scopus 로고    scopus 로고
    • Decrease in olfactory and taste receptor expression in the dorsolateral prefrontal cortex in chronic schizophrenia
    • Ansoleaga, B., Garcia-Esparcia, P., Pinacho, R., Haro, J.M., Ramos, B., Ferrer, I., Decrease in olfactory and taste receptor expression in the dorsolateral prefrontal cortex in chronic schizophrenia. J. Psychiatr. Res. 60 (2015), 109–116.
    • (2015) J. Psychiatr. Res. , vol.60 , pp. 109-116
    • Ansoleaga, B.1    Garcia-Esparcia, P.2    Pinacho, R.3    Haro, J.M.4    Ramos, B.5    Ferrer, I.6
  • 117
    • 85012918828 scopus 로고    scopus 로고
    • 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
  • 118
    • 79551571786 scopus 로고    scopus 로고
    • Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations
    • Vanni, S., Neri, M., Tavernelli, I., Rothlisberger, U., Predicting novel binding modes of agonists to β adrenergic receptors using all-atom molecular dynamics simulations. PLoS Comput. Biol., 7, 2011, e1001053.
    • (2011) PLoS Comput. Biol. , vol.7
    • Vanni, S.1    Neri, M.2    Tavernelli, I.3    Rothlisberger, U.4
  • 119
    • 41149132407 scopus 로고    scopus 로고
    • Comparative Protein Structure Modeling Using Modeller, Current Protocols in Bioinformatics
    • John Wiley & Sons, Inc
    • Eswar, N., Webb, B., Marti-Renom, M.A., Madhusudhan, M.S., Eramian, D., Shen, M.-y., Pieper, U., Sali, A., Comparative Protein Structure Modeling Using Modeller, Current Protocols in Bioinformatics. 2006, John Wiley & Sons, Inc, 5.6.1–5.6.30.
    • (2006) , pp. 5.6.1-5.6.30
    • Eswar, N.1    Webb, B.2    Marti-Renom, M.A.3    Madhusudhan, M.S.4    Eramian, D.5    Shen, M.-Y.6    Pieper, U.7    Sali, A.8
  • 120
    • 85019427531 scopus 로고    scopus 로고
    • Comparative protein structure modeling using MODELLER
    • Webb, B., Sali, A., Comparative protein structure modeling using MODELLER. Current Protocols in Protein Science 86 (2016), 2.9.1–2.9.37.
    • (2016) Current Protocols in Protein Science , vol.86 , pp. 2.9.1-2.9.37
    • Webb, B.1    Sali, A.2
  • 121
    • 43749109187 scopus 로고    scopus 로고
    • Crystal structure of squid rhodopsin
    • Murakami, M., Kouyama, T., Crystal structure of squid rhodopsin. Nature 453 (2008), 363–367.
    • (2008) Nature , vol.453 , pp. 363-367
    • Murakami, M.1    Kouyama, T.2
  • 122
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein− protein docking approach based on biochemical or biophysical information
    • Dominguez, C., Boelens, R., Bonvin, A.M., HADDOCK: a protein− protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003), 1731–1737.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 123
    • 27544504227 scopus 로고    scopus 로고
    • Evaluating the usefulness of protein structure models for molecular replacement
    • Giorgetti, A., Raimondo, D., Miele, A.E., Tramontano, A., Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics 21 (2005), ii72–ii76.
    • (2005) Bioinformatics , vol.21 , pp. ii72-ii76
    • Giorgetti, A.1    Raimondo, D.2    Miele, A.E.3    Tramontano, A.4
  • 124
    • 80051811105 scopus 로고    scopus 로고
    • Computational molecular biology approaches to ligand-target interactions
    • Lupieri, P., Hung Nguyen, C.H., Bafghi, Z.G., Giorgetti, A., Carloni, P., Computational molecular biology approaches to ligand-target interactions. HFSP J. 3 (2009), 228–239.
    • (2009) HFSP J. , vol.3 , pp. 228-239
    • Lupieri, P.1    Hung Nguyen, C.H.2    Bafghi, Z.G.3    Giorgetti, A.4    Carloni, P.5
  • 125
    • 85044556794 scopus 로고    scopus 로고
    • The Assessment of Methods for Protein Structure Prediction, Protein Structure Predictions
    • Humana Press
    • Tramontano, A., Cozzetto, D., Giorgetti, A., Raimondo, D., The Assessment of Methods for Protein Structure Prediction, Protein Structure Predictions. 2008, Humana Press, 43–57.
    • (2008) , pp. 43-57
    • Tramontano, A.1    Cozzetto, D.2    Giorgetti, A.3    Raimondo, D.4
  • 126
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR dock 2010 assessment
    • Kufareva, I., Rueda, M., Katritch, V., Stevens, Raymond C., Abagyan, R., Status of GPCR modeling and docking as reflected by community-wide GPCR dock 2010 assessment. Structure 19 (2011), 1108–1126.
    • (2011) Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Katritch, V.3    Stevens, R.C.4    Abagyan, R.5
  • 127
    • 84964600337 scopus 로고    scopus 로고
    • Structural modeling of G-protein coupled receptors: an overview on automatic web-servers
    • Busato, M., Giorgetti, A., Structural modeling of G-protein coupled receptors: an overview on automatic web-servers. Int. J. Biochem. Cell Biol. 77 (2016), 264–274.
    • (2016) Int. J. Biochem. Cell Biol. , vol.77 , pp. 264-274
    • Busato, M.1    Giorgetti, A.2
  • 128
    • 84878530705 scopus 로고    scopus 로고
    • 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
  • 133
    • 84864221004 scopus 로고    scopus 로고
    • 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
  • 136
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
    • Schüttelkopf, A.W., Van Aalten, D.M., PRODRG: a tool for high-throughput crystallography of protein–ligand complexes. Acta Cryst. D 60 (2004), 1355–1363.
    • (2004) Acta Cryst. D , vol.60 , pp. 1355-1363
    • Schüttelkopf, A.W.1    Van Aalten, D.M.2
  • 137
    • 0000667030 scopus 로고
    • Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
    • Cornell, W.D., Cieplak, P., Bayly, C.I., Kollmann, P.A., Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation. J. Am. Chem. Soc. 115 (1993), 9620–9631.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 9620-9631
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3    Kollmann, P.A.4
  • 138
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., 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
  • 141
    • 58149170454 scopus 로고    scopus 로고
    • Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins
    • Cascella, M., Neri, M.A., Carloni, P., Peraro, M.D., Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins. J. Chem. Theor. Comput. 4 (2008), 1378–1385.
    • (2008) J. Chem. Theor. Comput. , vol.4 , pp. 1378-1385
    • Cascella, M.1    Neri, M.A.2    Carloni, P.3    Peraro, M.D.4
  • 142
    • 85034105418 scopus 로고    scopus 로고
    • Open boundary simulations of proteins and their hydration shells by Hamiltonian adaptive resolution scheme
    • Tarenzi, T., Calandrini, V., Potestio, R., Giorgetti, A., Carloni, P., Open boundary simulations of proteins and their hydration shells by Hamiltonian adaptive resolution scheme. J. Chem. Theor. Comput. 13 (2017), 5647–5657.
    • (2017) J. Chem. Theor. Comput. , vol.13 , pp. 5647-5657
    • Tarenzi, T.1    Calandrini, V.2    Potestio, R.3    Giorgetti, A.4    Carloni, P.5
  • 144
    • 80052158550 scopus 로고    scopus 로고
    • 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
  • 145
    • 84951743686 scopus 로고    scopus 로고
    • Comparing Class A GPCRs to bitter taste receptors: structural motifs, ligand interactions and agonist-to-antagonist ratios
    • 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. Meth. Cell Biol. 132 (2016), 401–427.
    • (2016) Meth. Cell Biol. , 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.