메뉴 건너뛰기




Volumn 22, Issue 2, 2017, Pages

Recent advances and applications of molecular docking to g protein-coupled receptors

Author keywords

Docking; Drug design; GPCRs

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND; PROTEIN BINDING;

EID: 85018182815     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules22020340     Document Type: Review
Times cited : (55)

References (165)
  • 1
    • 84939156572 scopus 로고    scopus 로고
    • Thematic minireview series: New directions in g protein-coupled receptor pharmacology
    • CrossRef
    • Dohlman, H.G. Thematic Minireview Series: New Directions in G Protein-coupled Receptor Pharmacology. J. Biol. Chem. 2015, 290, 19469-19470. [CrossRef].
    • (2015) J. Biol. Chem , vol.290 , pp. 19469-19470
    • Dohlman, H.G.1
  • 2
    • 36949011636 scopus 로고    scopus 로고
    • The G protein-coupled receptor subset of the rat genome
    • [CrossRef] [PubMed]
    • Gloriam, D.E.; Fredriksson, R.; Schiöth, H.B. The G protein-coupled receptor subset of the rat genome. BMC Genom. 2007, 8, 338. [CrossRef] [PubMed].
    • (2007) BMC Genom , vol.8 , pp. 338
    • Gloriam, D.E.1    Fredriksson, R.2    Schiöth, H.B.3
  • 3
    • 0028262380 scopus 로고
    • Two hypotheses-one answer. Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukaryotic G-protein-coupled receptors
    • CrossRef
    • Soppa, J. Two hypotheses-one answer. Sequence comparison does not support an evolutionary link between halobacterial retinal proteins including bacteriorhodopsin and eukaryotic G-protein-coupled receptors. FEBS Lett. 1994, 342, 7-11. [CrossRef].
    • (1994) FEBS Lett. , vol.342 , pp. 7-11
    • Soppa, J.1
  • 4
    • 33847673071 scopus 로고    scopus 로고
    • G protein-coupled time travel: Evolutionary aspects of GPCR research
    • [CrossRef] [PubMed]
    • Römpler, H.; Stäubert, C.; Thor, D.; Schulz, A.; Hofreiter, M.; Schöneberg, T. G protein-coupled time travel: Evolutionary aspects of GPCR research. Mol. Interv. 2007, 7, 17-25. [CrossRef] [PubMed].
    • (2007) Mol. Interv , vol.7 , pp. 17-25
    • Römpler, H.1    Stäubert, C.2    Thor, D.3    Schulz, A.4    Hofreiter, M.5    Schöneberg, T.6
  • 5
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
    • [CrossRef] [PubMed]
    • 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. 2003, 63, 1256-1272. [CrossRef] [PubMed].
    • (2003) Mol. Pharmacol. , vol.63 , pp. 1256-1272
    • Fredriksson, R.1    Lagerström, M.C.2    Lundin, L.-G.3    Schiöth, H.B.4
  • 6
    • 85018174630 scopus 로고    scopus 로고
    • Chapter 4-GTP-binding Proteins and Signal Transduction
    • (Second Edition); Gomperts, B.D. Kramer, I.M. Tatham, P.E.R. Eds. Academic Press: San Diego, CA, USA
    • Gomperts, B.D.; Kramer, I.M.; Tatham, P.E.R. Chapter 4-GTP-binding Proteins and Signal Transduction. In Signal Transduction (Second Edition); Gomperts, B.D., Kramer, I.M., Tatham, P.E.R., Eds.; Academic Press: San Diego, CA, USA, 2009; pp. 81-129.
    • (2009) Signal Transduction , pp. 81-129
    • Gomperts, B.D.1    Kramer, I.M.2    Tatham, P.E.R.3
  • 7
    • 31144431614 scopus 로고    scopus 로고
    • Protein-coupled signal transmission pathways
    • Wiley-VCH Verlag GmbH & Co. KGaA:Weinheim, Germany
    • Krauss, G. G Protein-Coupled Signal Transmission Pathways. In Biochemistry of Signal Transduction and Regulation; Wiley-VCH Verlag GmbH & Co. KGaA:Weinheim, Germany, 2003; pp. 179-229.
    • (2003) Biochemistry of Signal Transduction and Regulation , pp. 179-229
    • Krauss, G.G.1
  • 8
    • 84952984381 scopus 로고    scopus 로고
    • Biased agonism: An emerging paradigm in GPCR drug discovery
    • [CrossRef] [PubMed]
    • Rankovic, Z.; Brust, T.F.; Bohn, L.M. Biased agonism: An emerging paradigm in GPCR drug discovery. Bioorg. Med. Chem. Lett. 2016, 26, 241-250. [CrossRef] [PubMed].
    • (2016) Bioorg. Med. Chem. Lett. , vol.26 , pp. 241-250
    • Rankovic, Z.1    Brust, T.F.2    Bohn, L.M.3
  • 9
    • 84930857717 scopus 로고    scopus 로고
    • Minireview: Role of intracellular scaffolding proteins in the regulation of endocrine G protein-coupled receptor signaling
    • [CrossRef] [PubMed]
    • Walther, C.; Ferguson, S.S.G. Minireview: Role of intracellular scaffolding proteins in the regulation of endocrine G protein-coupled receptor signaling. Mol. Endocrinol. 2015, 29, 814-830. [CrossRef] [PubMed].
    • (2015) Mol. Endocrinol. , vol.29 , pp. 814-830
    • Walther, C.1    Ferguson, S.S.G.2
  • 10
    • 0037285444 scopus 로고    scopus 로고
    • Rhodopsin structure, dynamics, and activation: A perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking
    • PubMed
    • Hubbell, W.L.; Altenbach, C.; Hubbell, C.M.; Khorana, H.G. Rhodopsin structure, dynamics, and activation: A perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking. Adv. Protein Chem. 2003, 63, 243-290. [PubMed].
    • (2003) Adv. Protein Chem , vol.63 , pp. 243-290
    • Hubbell, W.L.1    Altenbach, C.2    Hubbell, C.M.3    Khorana, H.G.4
  • 11
    • 0029907599 scopus 로고    scopus 로고
    • Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin
    • [CrossRef] [PubMed]
    • Farrens, D.L.; Altenbach, C.; Yang, K.; Hubbell, W.L.; Khorana, H.G. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 1996, 274, 768-770. [CrossRef] [PubMed].
    • (1996) Science , vol.274 , pp. 768-770
    • Farrens, D.L.1    Altenbach, C.2    Yang, K.3    Hubbell, W.L.4    Khorana, H.G.5
  • 12
    • 0030859541 scopus 로고    scopus 로고
    • Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor
    • [CrossRef] [PubMed]
    • Gether, U.; Lin, S.; Ghanouni, P.; Ballesteros, J.A.;Weinstein, H.; Kobilka, B.K. Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor. EMBO J. 1997, 16, 6737-6747. [CrossRef] [PubMed].
    • (1997) EMBO J. , vol.16 , pp. 6737-6747
    • Gether, U.1    Lin, S.2    Ghanouni, P.3    Ballesteros, J.A.4    Weinstein, H.5    Kobilka, B.K.6
  • 13
    • 33746382921 scopus 로고    scopus 로고
    • Coupling ligand structure to specific conformational switches in the beta2-Adrenoceptor
    • [CrossRef] [PubMed]
    • Yao, X.; Parnot, C.; Deupi, X.; Ratnala, V.R.P.; Swaminath, G.; Farrens, D.; Kobilka, B. Coupling ligand structure to specific conformational switches in the beta2-Adrenoceptor. Nat. Chem. Biol. 2006, 2, 417-422. [CrossRef] [PubMed].
    • (2006) Nat. Chem. Biol. , vol.2 , pp. 417-422
    • Yao, X.1    Parnot, C.2    Deupi, X.3    Ratnala, V.R.P.4    Swaminath, G.5    Farrens, D.6    Kobilka, B.7
  • 14
    • 44949236117 scopus 로고    scopus 로고
    • High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation
    • [CrossRef] [PubMed]
    • Altenbach, C.; Kusnetzow, A.K.; Ernst, O.P.; Hofmann, K.P.; Hubbell, W.L. High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation. Proc. Natl. Acad. Sci. USA 2008, 105, 7439-7444. [CrossRef] [PubMed].
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 7439-7444
    • Altenbach, C.1    Kusnetzow, A.K.2    Ernst, O.P.3    Hofmann, K.P.4    Hubbell, W.L.5
  • 17
    • 84858164791 scopus 로고    scopus 로고
    • Action of molecular switches in GPCRs-Theoretical and experimental studies
    • [CrossRef] [PubMed]
    • Trzaskowski, B.; Latek, D.; Yuan, S.; Ghoshdastider, U.; Debinski, A.; Filipek, S. Action of molecular switches in GPCRs-Theoretical and experimental studies. Curr. Med. Chem. 2012, 19, 1090-1109. [CrossRef] [PubMed].
    • (2012) Curr. Med. Chem , vol.19 , pp. 1090-1109
    • Trzaskowski, B.1    Latek, D.2    Yuan, S.3    Ghoshdastider, U.4    Debinski, A.5    Filipek, S.6
  • 18
    • 84988493297 scopus 로고    scopus 로고
    • Rational selection of the 3D structure of biomacromolecules for molecular docking studies on the mechanism of endocrine disruptor action
    • [CrossRef] [PubMed]
    • Yang, X.; Liu, H.; Liu, J.; Li, F.; Li, X.; Shi, L.; Chen, J. Rational Selection of the 3D Structure of Biomacromolecules for Molecular Docking Studies on the Mechanism of Endocrine Disruptor Action. Chem. Res. Toxicol. 2016, 29, 1565-1570. [CrossRef] [PubMed].
    • (2016) Chem. Res. Toxicol , vol.29 , pp. 1565-1570
    • Yang, X.1    Liu, H.2    Liu, J.3    Li, F.4    Li, X.5    Shi, L.6    Chen, J.7
  • 19
  • 20
    • 0018165127 scopus 로고
    • Computer analysis of protein-protein interaction
    • CrossRef
    • Wodak, S.J.; Janin, J. Computer analysis of protein-protein interaction. J. Mol. Biol. 1978, 124, 323-342. [CrossRef].
    • (1978) J. Mol. Biol. , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 21
    • 84885897981 scopus 로고    scopus 로고
    • Structure-based molecular modeling approaches to GPCR oligomerization
    • PubMed
    • Kaczor, A.A.; Selent, J.; Poso, A. Structure-based molecular modeling approaches to GPCR oligomerization. Methods Cell Biol. 2013, 117, 91-104. [PubMed].
    • (2013) Methods Cell Biol , vol.117 , pp. 91-104
    • Kaczor, A.A.1    Selent, J.2    Poso, A.3
  • 22
    • 84949520925 scopus 로고    scopus 로고
    • Advances in computational techniques to study GPCR-ligand recognition
    • [CrossRef] [PubMed]
    • Ciancetta, A.; Sabbadin, D.; Federico, S.; Spalluto, G.; Moro, S. Advances in Computational Techniques to Study GPCR-Ligand Recognition. Trends Pharmacol. Sci. 2015, 36, 878-890. [CrossRef] [PubMed].
    • (2015) Trends Pharmacol. Sci , vol.36 , pp. 878-890
    • Ciancetta, A.1    Sabbadin, D.2    Federico, S.3    Spalluto, G.4    Moro, S.5
  • 23
    • 77957899529 scopus 로고    scopus 로고
    • Advances and challenges in protein-ligand docking
    • [CrossRef] [PubMed]
    • Huang, S.-Y.; Zou, X. Advances and Challenges in Protein-Ligand Docking. Int. J. Mol. Sci. 2010, 11, 3016-3034. [CrossRef] [PubMed].
    • (2010) Int. J. Mol. Sci , vol.11 , pp. 3016-3034
    • Huang, S.-Y.1    Zou, X.2
  • 25
    • 84952815472 scopus 로고    scopus 로고
    • A new method for navigating optimal direction for pulling ligand from binding pocket: Application to ranking binding affinity by steered molecular dynamics
    • [CrossRef] [PubMed]
    • Vuong, Q.V.; Nguyen, T.T.; Li, M.S. A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics. J. Chem. Inf. Model. 2015, 55, 2731-2738. [CrossRef] [PubMed].
    • (2015) J. Chem. Inf. Model , vol.55 , pp. 2731-2738
    • Vuong, Q.V.1    Nguyen, T.T.2    Li, M.S.3
  • 26
    • 84905732337 scopus 로고    scopus 로고
    • Advances in GPCR modeling evaluated by the GPCR dock 2013 assessment: Meeting new challenges
    • Participants of GPCR Dock 2013
    • Kufareva, I.; Katritch, V.; Participants of GPCR Dock 2013; Stevens, R.C.; Abagyan, R. Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: Meeting new challenges. Structure 2014, 22, 1120-1139.
    • (2014) Structure , vol.22 , pp. 1120-1139
    • Kufareva, I.1    Katritch, V.2    Stevens, R.C.3    Abagyan, R.4
  • 30
    • 84910633308 scopus 로고    scopus 로고
    • A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2
    • [CrossRef] [PubMed]
    • Perez-Aguilar, J.M.; Shan, J.; LeVine, M.V.; Khelashvili, G.; Weinstein, H. A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2. J. Am. Chem. Soc. 2014, 136, 16044-16054. [CrossRef] [PubMed].
    • (2014) J. Am. Chem. Soc. , vol.136 , pp. 16044-16054
    • Perez-Aguilar, J.M.1    Shan, J.2    LeVine, M.V.3    Khelashvili, G.4    Weinstein, H.5
  • 31
    • 84962419910 scopus 로고    scopus 로고
    • Interplay between two allosteric sites and their influence on agonist binding in human μ opioid receptor
    • [CrossRef] [PubMed]
    • Bartuzi, D.; Kaczor, A.A.; Matosiuk, D. Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor. J. Chem. Inf. Model. 2016, 56, 563-570. [CrossRef] [PubMed].
    • (2016) J. Chem. Inf. Model , vol.56 , pp. 563-570
    • Bartuzi, D.1    Kaczor, A.A.2    Matosiuk, D.3
  • 32
    • 84979862649 scopus 로고    scopus 로고
    • What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands?
    • [CrossRef] [PubMed]
    • Michino, M.; Beuming, T.; Donthamsetti, P.; Newman, A.H.; Javitch, J.A.; Shi, L. What Can Crystal Structures of Aminergic Receptors Tell Us about Designing Subtype-Selective Ligands? Pharmacol. Rev. 2015, 67, 198-213. [CrossRef] [PubMed].
    • (2015) Pharmacol. Rev. , vol.67 , pp. 198-213
    • Michino, M.1    Beuming, T.2    Donthamsetti, P.3    Newman, A.H.4    Javitch, J.A.5    Shi, L.6
  • 33
    • 77957055780 scopus 로고
    • [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
    • Sealfon, S.C. Ed. Receptor Molecular Biology; Academic Press: San Diego, CA, USA
    • Ballesteros, J.A.; Weinstein, H. [19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors. In Methods in Neurosciences; Sealfon, S.C., Ed.; Receptor Molecular Biology; Academic Press: San Diego, CA, USA, 1995; Volume 25, pp. 366-428.
    • (1995) Methods in Neurosciences , vol.25 , pp. 366-428
    • Ballesteros, J.A.1    Weinstein, H.2
  • 34
    • 84925392495 scopus 로고    scopus 로고
    • Molecular docking screening using agonist-bound GPCR structures: Probing the A 2A adenosine receptor
    • [CrossRef] [PubMed]
    • Rodríguez, D.; Gao, Z.-G.; Moss, S.M.; Jacobson, K.A.; Carlsson, J. Molecular Docking Screening Using Agonist-Bound GPCR Structures: Probing the A 2A Adenosine Receptor. J. Chem. Inf. Model. 2015, 55, 550-563. [CrossRef] [PubMed].
    • (2015) J. Chem. Inf. Model. , vol.55 , pp. 550-563
    • Rodríguez, D.1    Gao, Z.-G.2    Moss, S.M.3    Jacobson, K.A.4    Carlsson, J.5
  • 35
    • 0027053611 scopus 로고
    • POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • CrossRef
    • Levitt, D.G.; Banaszak, L.J. POCKET: A Computer Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino Acids. J. Mol. Graph. 1992, 10, 229-234. [CrossRef].
    • (1992) J. Mol. Graph , vol.10 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 36
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • CrossRef
    • Laskowski, R.A. SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 1995, 13, 323-330. [CrossRef].
    • (1995) J. Mol. Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 37
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • [CrossRef] [PubMed]
    • Brady, G.P.; Stouten, P.F. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 2000, 14, 383-401. [CrossRef] [PubMed].
    • (2000) J. Comput. Aided Mol. des , vol.14 , pp. 383-401
    • Brady, G.P.1    Stouten, P.F.2
  • 38
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: An open source platform for ligand pocket detection
    • [CrossRef] [PubMed]
    • Le Guilloux, V.; Schmidtke, P.; Tuffery, P. Fpocket: An open source platform for ligand pocket detection. BMC Bioinform. 2009, 10, 168. [CrossRef] [PubMed].
    • (2009) BMC Bioinform. , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 39
    • 84880921576 scopus 로고    scopus 로고
    • E find site: Improved prediction of ligand binding sites in protein models using meta-Threading, machine learning and auxiliary ligands
    • [CrossRef] [PubMed]
    • Brylinski, M.; Feinstein, W.P. e Find Site: Improved prediction of ligand binding sites in protein models using meta-Threading, machine learning and auxiliary ligands. J. Comput. Aided Mol. Des. 2013, 27, 551-567. [CrossRef] [PubMed].
    • (2013) J. Comput. Aided Mol. des , vol.27 , pp. 551-567
    • Brylinski, M.1    Feinstein, W.P.2
  • 40
    • 84874754249 scopus 로고    scopus 로고
    • A poc: Large-scale identification of similar protein pockets
    • [CrossRef] [PubMed]
    • Gao, M.; Skolnick, J. A Poc: Large-scale identification of similar protein pockets. Bioinformatics 2013, 29, 597-604. [CrossRef] [PubMed].
    • (2013) Bioinformatics , vol.29 , pp. 597-604
    • Gao, M.1    Skolnick, J.2
  • 42
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
    • CrossRef
    • Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olson, A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662. [CrossRef].
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 43
    • 76149120388 scopus 로고    scopus 로고
    • Auto dock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • [CrossRef] [PubMed]
    • Trott, O.; Olson, A.J. Auto Dock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461. [CrossRef] [PubMed].
    • (2010) J. Comput. Chem , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 44
    • 84973646291 scopus 로고    scopus 로고
    • Chemical Computing Group Inc.: Montreal, QC, Canada
    • Molecular Operating Environment (MOE); Chemical Computing Group Inc.: Montreal, QC, Canada, 2016.
    • (2016) Molecular Operating Environment (MOE)
  • 45
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • [CrossRef] [PubMed]
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489. [CrossRef] [PubMed].
    • (1996) J. Mol. Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 48
    • 8844263008 scopus 로고    scopus 로고
    • Docking and scoring in virtual screening for drug discovery: Methods and applications
    • [CrossRef] [PubMed]
    • Kitchen, D.B.; Decornez, H.; Furr, J.R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: Methods and applications. Nat. Rev. Drug Discov. 2004, 3, 935-949. [CrossRef] [PubMed].
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 935-949
    • Kitchen, D.B.1    Decornez, H.2    Furr, J.R.3    Bajorath, J.4
  • 49
    • 70349932423 scopus 로고    scopus 로고
    • Auto dock4 and autodock tools4: Automated docking with selective receptor flexibility
    • [CrossRef] [PubMed]
    • Morris, G.M.; Huey, R.; Lindstrom, W.; Sanner, M.F.; Belew, R.K.; Goodsell, D.S.; Olson, A.J. Auto Dock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comput. Chem. 2009, 30, 2785-2791. [CrossRef] [PubMed].
    • (2009) J. Comput. Chem. , vol.30 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3    Sanner, M.F.4    Belew, R.K.5    Goodsell, D.S.6    Olson, A.J.7
  • 50
    • 79251557517 scopus 로고    scopus 로고
    • Evaluation of 1-Arylpiperazine derivative of hydroxybenzamides as 5-HT1A and 5-HT7 serotonin receptor ligands: An experimental and molecular modeling approach
    • CrossRef
    • Kowalski, P.; Jáskowska, J.; Bojarski, A.J.; Duszý nska, B.; Bucki, A.; Kołaczkowski, M. Evaluation of 1-Arylpiperazine derivative of hydroxybenzamides as 5-HT1A and 5-HT7 serotonin receptor ligands: An experimental and molecular modeling approach. J. Heterocycl. Chem. 2011, 48, 192-198. [CrossRef].
    • (2011) J. Heterocycl. Chem. , vol.48 , pp. 192-198
    • Kowalski, P.1    Jáskowska, J.2    Bojarski, A.J.3    Duszý Nska, B.4    Bucki, A.5    Kołaczkowski, M.6
  • 51
    • 84939256123 scopus 로고    scopus 로고
    • NMR-Assisted molecular docking methodologies
    • [CrossRef] [PubMed]
    • Sturlese, M.; Bellanda, M.; Moro, S. NMR-Assisted Molecular Docking Methodologies. Mol. Inform. 2015, 34, 513-525. [CrossRef] [PubMed].
    • (2015) Mol. Inform. , vol.34 , pp. 513-525
    • Sturlese, M.1    Bellanda, M.2    Moro, S.3
  • 52
    • 67349088738 scopus 로고    scopus 로고
    • Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008
    • GPCR Dock 2008 participants, [CrossRef] [PubMed]
    • Michino, M.; Abola, E.; GPCR Dock 2008 participants; Brooks, C.L.; Dixon, J.S.; Moult, J.; Stevens, R.C. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nat. Rev. Drug Discov. 2009, 8, 455-463. [CrossRef] [PubMed].
    • (2009) Nat. Rev. Drug Discov. , vol.8 , pp. 455-463
    • Michino, M.1    Abola, E.2    Brooks, C.L.3    Dixon, J.S.4    Moult, J.5    Stevens, R.C.6
  • 53
    • 80051521545 scopus 로고    scopus 로고
    • Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
    • GPCR Dock 2010 participants
    • Kufareva, I.; Rueda, M.; Katritch, V.; Stevens, R.C.; Abagyan, R.; GPCR Dock 2010 participants. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure 2011, 19, 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
  • 54
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • CrossRef
    • Totrov, M.; Abagyan, R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997, 29 (Suppl.1), 215-220. [CrossRef].
    • (1997) Proteins , vol.29 , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 56
    • 84988411282 scopus 로고    scopus 로고
    • Dock bench as docking selector tool: The lesson learned from D3R grand challenge 2015
    • [CrossRef] [PubMed]
    • Salmaso, V.; Sturlese, M.; Cuzzolin, A.; Moro, S. DockBench as docking selector tool: The lesson learned from D3R Grand Challenge 2015. J. Comput. Aided Mol. Des. 2016, 30, 773-789. [CrossRef] [PubMed].
    • (2016) J. Comput. Aided Mol. des , vol.30 , pp. 773-789
    • Salmaso, V.1    Sturlese, M.2    Cuzzolin, A.3    Moro, S.4
  • 58
    • 67651204566 scopus 로고    scopus 로고
    • Structure-based design, synthesis, and biochemical and pharmacological characterization of novel salvinorin A analogues as active state probes of the kappa-opioid receptor
    • [CrossRef] [PubMed]
    • Yan, F.; Bikbulatov, R.V.; Mocanu, V.; Dicheva, N.; Parker, C.E.; Wetsel, W.C.; Mosier, P.D.; Westkaemper, R.B.; Allen, J.A.; Zjawiony, J.K.; et al. Structure-based design, synthesis, and biochemical and pharmacological characterization of novel salvinorin A analogues as active state probes of the kappa-opioid receptor. Biochemistry (Mosc.) 2009, 48, 6898-6908. [CrossRef] [PubMed].
    • (2009) Biochemistry (Mosc.) , vol.48 , pp. 6898-6908
    • Yan, F.1    Bikbulatov, R.V.2    Mocanu, V.3    Dicheva, N.4    Parker, C.E.5    Wetsel, W.C.6    Mosier, P.D.7    Westkaemper, R.B.8    Allen, J.A.9    Zjawiony, J.K.10
  • 59
    • 84930189471 scopus 로고    scopus 로고
    • Anchor dock: Blind and flexible anchor-driven peptide docking
    • [CrossRef] [PubMed]
    • Ben-Shimon, A.; Niv, M.Y. Anchor Dock: Blind and Flexible Anchor-Driven Peptide Docking. Structure 2015, 23, 929-940. [CrossRef] [PubMed].
    • (2015) Structure , vol.23 , pp. 929-940
    • Ben-Shimon, A.1    Niv, M.Y.2
  • 60
    • 84989824640 scopus 로고    scopus 로고
    • Fully blind docking at the atomic level for protein-peptide complex structure prediction
    • [CrossRef] [PubMed]
    • Yan, C.; Xu, X.; Zou, X. Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction. Structure 2016, 24, 1842-1853. [CrossRef] [PubMed].
    • (2016) Structure , vol.24 , pp. 1842-1853
    • Yan, C.1    Xu, X.2    Zou, X.3
  • 61
    • 84979863225 scopus 로고    scopus 로고
    • Galaxy pep dock: A protein-peptide docking tool based on interaction similarity and energy optimization
    • [CrossRef] [PubMed]
    • Lee, H.; Heo, L.; Lee, M.S.; Seok, C. Galaxy Pep Dock: A protein-peptide docking tool based on interaction similarity and energy optimization. Nucleic Acids Res. 2015, 43, W431-W435. [CrossRef] [PubMed].
    • (2015) Nucleic Acids Res. , vol.43 , pp. W431-W435
    • Lee, H.1    Heo, L.2    Lee, M.S.3    Seok, C.4
  • 62
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • [CrossRef] [PubMed]
    • Jain, A.N. Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine. J. Med. Chem. 2003, 46, 499-511. [CrossRef] [PubMed].
    • (2003) J. Med. Chem. , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 63
    • 84955443785 scopus 로고    scopus 로고
    • LEADS-PEP: A benchmark data set for assessment of peptide docking performance
    • [CrossRef] [PubMed]
    • Hauser, A.S.; Windshügel, B. LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance. J. Chem. Inf. Model. 2016, 56, 188-200. [CrossRef] [PubMed].
    • (2016) J. Chem. Inf. Model , vol.56 , pp. 188-200
    • Hauser, A.S.1    Windshügel, B.2
  • 65
    • 78650667884 scopus 로고    scopus 로고
    • Accounting for water molecules in drug design
    • [CrossRef] [PubMed]
    • Wong, S.E.; Lightstone, F.C. Accounting for water molecules in drug design. Expert Opin. Drug Discov. 2011, 6, 65-74. [CrossRef] [PubMed].
    • (2011) Expert Opin. Drug Discov , vol.6 , pp. 65-74
    • Wong, S.E.1    Lightstone, F.C.2
  • 66
    • 84939813976 scopus 로고    scopus 로고
    • Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description
    • [CrossRef] [PubMed]
    • Spyrakis, F.; Cavasotto, C.N. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch. Biochem. Biophys. 2015, 583, 105-119. [CrossRef] [PubMed].
    • (2015) Arch. Biochem. Biophys , vol.583 , pp. 105-119
    • Spyrakis, F.1    Cavasotto, C.N.2
  • 67
    • 77949358478 scopus 로고    scopus 로고
    • The role of water molecules in computational drug design
    • [CrossRef] [PubMed]
    • De Beer, S.B.A.; Vermeulen, N.P.E.; Oostenbrink, C. The role of water molecules in computational drug design. Curr. Top. Med. Chem. 2010, 10, 55-66. [CrossRef] [PubMed].
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 55-66
    • De Beer, S.B.A.1    Vermeulen, N.P.E.2    Oostenbrink, C.3
  • 68
    • 50249094315 scopus 로고    scopus 로고
    • Exploiting ordered waters in molecular docking
    • [CrossRef] [PubMed]
    • Huang, N.; Shoichet, B.K. Exploiting ordered waters in molecular docking. J. Med. Chem. 2008, 51, 4862-4865. [CrossRef] [PubMed].
    • (2008) J. Med. Chem , vol.51 , pp. 4862-4865
    • Huang, N.1    Shoichet, B.K.2
  • 69
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • [CrossRef] [PubMed]
    • Goodford, P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857. [CrossRef] [PubMed].
    • (1985) J. Med. Chem , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 70
    • 33645106609 scopus 로고    scopus 로고
    • Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: Predictive tools for characterizing the roles of water in biomolecules
    • [CrossRef] [PubMed]
    • Amadasi, A.; Spyrakis, F.; Cozzini, P.; Abraham, D.J.; Kellogg, G.E.; Mozzarelli, A. Mapping the energetics of water-protein and water-ligand interactions with the "natural" HINT forcefield: Predictive tools for characterizing the roles of water in biomolecules. J. Mol. Biol. 2006, 358, 289-309. [CrossRef] [PubMed].
    • (2006) J. Mol. Biol. , vol.358 , pp. 289-309
    • Amadasi, A.1    Spyrakis, F.2    Cozzini, P.3    Abraham, D.J.4    Kellogg, G.E.5    Mozzarelli, A.6
  • 71
    • 0033047007 scopus 로고    scopus 로고
    • Super star: A knowledge-based approach for identifying interaction sites in proteins
    • CrossRef
    • Verdonk, M.L.; Cole, J.C.; Taylor, R. Super Star: A knowledge-based approach for identifying interaction sites in proteins. J. Mol. Biol. 1999, 289, 1093-1108. [CrossRef].
    • (1999) J. Mol. Biol. , vol.289 , pp. 1093-1108
    • Verdonk, M.L.1    Cole, J.C.2    Taylor, R.3
  • 72
    • 70349683018 scopus 로고    scopus 로고
    • Prediction of the water content in protein binding sites
    • [CrossRef] [PubMed]
    • Michel, J.; Tirado-Rives, J.; Jorgensen, W.L. Prediction of the water content in protein binding sites. J. Phys. Chem. B 2009, 113, 13337-13346. [CrossRef] [PubMed].
    • (2009) J. Phys. Chem. B , vol.113 , pp. 13337-13346
    • Michel, J.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 73
    • 33846524439 scopus 로고    scopus 로고
    • Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
    • [CrossRef] [PubMed]
    • Young, T.; Abel, R.; Kim, B.; Berne, B.J.; Friesner, R.A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc. Natl. Acad. Sci. USA 2007, 104, 808-813. [CrossRef] [PubMed].
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 808-813
    • Young, T.1    Abel, R.2    Kim, B.3    Berne, B.J.4    Friesner, R.A.5
  • 74
    • 84873635524 scopus 로고    scopus 로고
    • Water PMF for predicting the properties of water molecules in protein binding site
    • [CrossRef] [PubMed]
    • Zheng, M.; Li, Y.; Xiong, B.; Jiang, H.; Shen, J. Water PMF for predicting the properties of water molecules in protein binding site. J. Comput. Chem. 2013, 34, 583-592. [CrossRef] [PubMed].
    • (2013) J. Comput. Chem. , vol.34 , pp. 583-592
    • Zheng, M.1    Li, Y.2    Xiong, B.3    Jiang, H.4    Shen, J.5
  • 75
    • 34247263219 scopus 로고    scopus 로고
    • A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for ligands and proteins (FLAP): Theory and application
    • [CrossRef] [PubMed]
    • Baroni, M.; Cruciani, G.; Sciabola, S.; Perruccio, F.; Mason, J.S. A common reference framework for analyzing/comparing proteins and ligands. Fingerprints for Ligands and Proteins (FLAP): Theory and application. J. Chem. Inf. Model. 2007, 47, 279-294. [CrossRef] [PubMed].
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 279-294
    • Baroni, M.1    Cruciani, G.2    Sciabola, S.3    Perruccio, F.4    Mason, J.S.5
  • 76
    • 84991461535 scopus 로고    scopus 로고
    • Incorporating QM and solvation into docking for applications to GPCR targets
    • CrossRef
    • Kim, M.; Cho, A.E. Incorporating QM and solvation into docking for applications to GPCR targets. Phys. Chem. Chem. Phys. 2016, 18, 28281-28289. [CrossRef].
    • (2016) Phys. Chem. Chem. Phys , vol.18 , pp. 28281-28289
    • Kim, M.1    Cho, A.E.2
  • 77
    • 84903312448 scopus 로고    scopus 로고
    • Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor
    • CrossRef
    • Lenselink, E.B.; Beuming, T.; Sherman, W.; van Vlijmen, H.W.T.; IJzerman, A.P. Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor. J. Chem. Inf. Model. 2014, 54, 1737-1746. [CrossRef].
    • (2014) J. Chem. Inf. Model , vol.54 , pp. 1737-1746
    • Lenselink, E.B.1    Beuming, T.2    Sherman, W.3    Van Vlijmen, H.W.T.4    I'Jzerman, A.P.5
  • 78
    • 84874299846 scopus 로고    scopus 로고
    • Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: The use of water map
    • [CrossRef] [PubMed]
    • Yang, Y.; Lightstone, F.C.; Wong, S.E. Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: The use ofWaterMap. Expert Opin. Drug Discov. 2013, 8, 277-287. [CrossRef] [PubMed].
    • (2013) Expert Opin. Drug Discov , vol.8 , pp. 277-287
    • Yang, Y.1    Lightstone, F.C.2    Wong, S.E.3
  • 79
    • 84860505658 scopus 로고    scopus 로고
    • New insights from structural biology into the druggability of G protein-coupled receptors
    • [CrossRef] [PubMed]
    • Mason, J.S.; Bortolato, A.; Congreve, M.; Marshall, F.H. New insights from structural biology into the druggability of G protein-coupled receptors. Trends Pharmacol. Sci. 2012, 33, 249-260. [CrossRef] [PubMed].
    • (2012) Trends Pharmacol. Sci. , vol.33 , pp. 249-260
    • Mason, J.S.1    Bortolato, A.2    Congreve, M.3    Marshall, F.H.4
  • 80
    • 84869987897 scopus 로고    scopus 로고
    • The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations
    • [CrossRef] [PubMed]
    • Yuan, S.; Ghoshdastider, U.; Trzaskowski, B.; Latek, D.; Debinski, A.; Pulawski, W.; Wu, R.; Gerke, V.; Filipek, S. The role of water in activation mechanism of human N-formyl peptide receptor 1 (FPR1) based on molecular dynamics simulations. Plos One 2012, 7, e47114. [CrossRef] [PubMed].
    • (2012) Plos One , vol.7 , pp. e47114
    • Yuan, S.1    Ghoshdastider, U.2    Trzaskowski, B.3    Latek, D.4    Debinski, A.5    Pulawski, W.6    Wu, R.7    Gerke, V.8    Filipek, S.9
  • 81
    • 77955869797 scopus 로고    scopus 로고
    • Hydration site thermodynamics explain SARs for triazolylpurines analogues binding to the A2A receptor
    • [CrossRef] [PubMed]
    • Higgs, C.; Beuming, T.; Sherman, W. Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor. ACS Med. Chem. Lett. 2010, 1, 160-164. [CrossRef] [PubMed].
    • (2010) ACS Med. Chem. Lett , vol.1 , pp. 160-164
    • Higgs, C.1    Beuming, T.2    Sherman, W.3
  • 83
    • 65549163531 scopus 로고    scopus 로고
    • Recent advances in structure-based virtual screening of G-protein coupled receptors
    • [CrossRef] [PubMed]
    • Ananthan, S.; Zhang, W.; Hobrath, J.V. Recent advances in structure-based virtual screening of G-protein coupled receptors. AAPS J. 2009, 11, 178-185. [CrossRef] [PubMed].
    • (2009) AAPS J , vol.11 , pp. 178-185
    • Ananthan, S.1    Zhang, W.2    Hobrath, J.V.3
  • 84
    • 84860513814 scopus 로고    scopus 로고
    • Structure-based drug screening for G-protein-coupled receptors
    • [CrossRef] [PubMed]
    • Shoichet, B.K.; Kobilka, B.K. Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol. Sci. 2012, 33, 268-272. [CrossRef] [PubMed].
    • (2012) Trends Pharmacol. Sci. , vol.33 , pp. 268-272
    • Shoichet, B.K.1    Kobilka, B.K.2
  • 85
    • 84871539979 scopus 로고    scopus 로고
    • Current assessment of docking into GPCR crystal structures and homology models: Successes, challenges, and guidelines
    • [CrossRef] [PubMed]
    • Beuming, T.; Sherman, W. Current assessment of docking into GPCR crystal structures and homology models: Successes, challenges, and guidelines. J. Chem. Inf. Model. 2012, 52, 3263-3277. [CrossRef] [PubMed].
    • (2012) J. Chem. Inf. Model , vol.52 , pp. 3263-3277
    • Beuming, T.1    Sherman, W.2
  • 86
    • 71749086377 scopus 로고    scopus 로고
    • G protein-coupled receptors: Target-based in silico screening
    • [CrossRef] [PubMed]
    • Senderowitz, H.; Marantz, Y. G Protein-Coupled Receptors: Target-based in silico screening. Curr. Pharm. Des. 2009, 15, 4049-4068. [CrossRef] [PubMed].
    • (2009) Curr. Pharm. Des. , vol.15 , pp. 4049-4068
    • Senderowitz, H.1    Marantz, Y.2
  • 87
    • 84863247761 scopus 로고    scopus 로고
    • Structure-based design in the GPCR target space
    • [CrossRef] [PubMed]
    • Kontoyianni, M.; Liu, Z. Structure-based design in the GPCR target space. Curr. Med. Chem. 2012, 19, 544-556. [CrossRef] [PubMed].
    • (2012) Curr. Med. Chem , vol.19 , pp. 544-556
    • Kontoyianni, M.1    Liu, Z.2
  • 88
    • 84934441026 scopus 로고    scopus 로고
    • From three-dimensional GPCR structure to rational ligand discovery
    • PubMed
    • Kooistra, A.J.; Leurs, R.; de Esch, I.J.P.; de Graaf, C. From three-dimensional GPCR structure to rational ligand discovery. Adv. Exp. Med. Biol. 2014, 796, 129-157. [PubMed].
    • (2014) Adv. Exp. Med. Biol. , vol.796 , pp. 129-157
    • Kooistra, A.J.1    Leurs, R.2    De Esch, I.J.P.3    De Graaf, C.4
  • 90
    • 84875431627 scopus 로고    scopus 로고
    • Ligand-optimized homology models of D1 and D2 dopamine receptors: Application for virtual screening
    • [CrossRef] [PubMed]
    • Kołaczkowski, M.; Bucki, A.; Feder, M.; Pawłowski, M. Ligand-optimized homology models of D1 and D2 dopamine receptors: Application for virtual screening. J. Chem. Inf. Model. 2013, 53, 638-648. [CrossRef] [PubMed].
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 638-648
    • Kołaczkowski, M.1    Bucki, A.2    Feder, M.3    Pawłowski, M.4
  • 91
    • 84961262758 scopus 로고    scopus 로고
    • Structure-based virtual screening for dopamine D2 receptor ligands as potential antipsychotics
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Silva, A.G.; Loza, M.I.; Kolb, P.; Castro, M.; Poso, A. Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics. Chem Med Chem 2016, 11, 718-729. [CrossRef] [PubMed].
    • (2016) Chem Med Chem , vol.11 , pp. 718-729
    • Kaczor, A.A.1    Silva, A.G.2    Loza, M.I.3    Kolb, P.4    Castro, M.5    Poso, A.6
  • 92
    • 84940511935 scopus 로고    scopus 로고
    • Molecular modelling of human 5-hydroxytryptamine receptor (5-HT2A) and virtual screening studies towards the identification of agonist and antagonist molecules
    • [CrossRef] [PubMed]
    • Gandhimathi, A.; Sowdhamini, R. Molecular modelling of human 5-hydroxytryptamine receptor (5-HT2A) and virtual screening studies towards the identification of agonist and antagonist molecules. J. Biomol. Struct. Dyn. 2016, 34, 952-970. [CrossRef] [PubMed].
    • (2016) J. Biomol. Struct. Dyn. , vol.34 , pp. 952-970
    • Gandhimathi, A.1    Sowdhamini, R.2
  • 94
    • 84987875947 scopus 로고    scopus 로고
    • Discovery of novel antagonists of human neurotensin receptor 1 on the basis of ligand and protein structure
    • [CrossRef] [PubMed]
    • Zhang, G.;Wang, K.; Li, X.-D.; Zhang, D.-L.; Xu, F. Discovery of novel antagonists of human neurotensin receptor 1 on the basis of ligand and protein structure. Biomed. Pharmacother. Biomed. Pharmacother. 2016, 84, 147-157. [CrossRef] [PubMed].
    • (2016) Biomed. Pharmacother. Biomed. Pharmacother , vol.84 , pp. 147-157
    • Zhang, G.1    Wang, K.2    Li, X.-D.3    Zhang, D.-L.4    Xu, F.5
  • 95
    • 84908242789 scopus 로고    scopus 로고
    • Structure-based virtual screening of the nociceptin receptor: Hybrid docking and shape-based approaches for improved hit identification
    • [CrossRef] [PubMed]
    • Daga, P.R.; Polgar, W.E.; Zaveri, N.T. Structure-based virtual screening of the nociceptin receptor: Hybrid docking and shape-based approaches for improved hit identification. J. Chem. Inf. Model. 2014, 54, 2732-2743. [CrossRef] [PubMed].
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 2732-2743
    • Daga, P.R.1    Polgar, W.E.2    Zaveri, N.T.3
  • 96
    • 84969130017 scopus 로고    scopus 로고
    • GPCR-Bench: A benchmarking set and practitioners' guide for g protein-coupled receptor docking
    • [CrossRef] [PubMed]
    • Weiss, D.R.; Bortolato, A.; Tehan, B.; Mason, J.S. GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking. J. Chem. Inf. Model. 2016, 56, 642-651. [CrossRef] [PubMed].
    • (2016) J. Chem. Inf. Model. , vol.56 , pp. 642-651
    • Weiss, D.R.1    Bortolato, A.2    Tehan, B.3    Mason, J.S.4
  • 97
    • 84921838527 scopus 로고    scopus 로고
    • Fragment-based drug discovery and molecular docking in drug design
    • [CrossRef] [PubMed]
    • Wang, T.; Wu, M.-B.; Chen, Z.-J.; Chen, H.; Lin, J.-P.; Yang, L.-R. Fragment-based drug discovery and molecular docking in drug design. Curr. Pharm. Biotechnol. 2015, 16, 11-25. [CrossRef] [PubMed].
    • (2015) Curr. Pharm. Biotechnol , vol.16 , pp. 11-25
    • Wang, T.1    Wu, M.-B.2    Chen, Z.-J.3    Chen, H.4    Lin, J.-P.5    Yang, L.-R.6
  • 98
    • 84861078289 scopus 로고    scopus 로고
    • Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening
    • [CrossRef] [PubMed]
    • Tosh, D.K.; Phan, K.; Gao, Z.-G.; Gakh, A.A.; Xu, F.; Deflorian, F.; Abagyan, R.; Stevens, R.C.; Jacobson, K.A.; Katritch, V. Optimization of adenosine 5'-carboxamide derivatives as adenosine receptor agonists using structure-based ligand design and fragment screening. J. Med. Chem. 2012, 55, 4297-4308. [CrossRef] [PubMed].
    • (2012) J. Med. Chem , vol.55 , pp. 4297-4308
    • Tosh, D.K.1    Phan, K.2    Gao, Z.-G.3    Gakh, A.A.4    Xu, F.5    Deflorian, F.6    Abagyan, R.7    Stevens, R.C.8    Jacobson, K.A.9    Katritch, V.10
  • 100
    • 84953308120 scopus 로고    scopus 로고
    • Fragment-based discovery of subtype-selective adenosine receptor ligands from homology models
    • [CrossRef] [PubMed]
    • Ranganathan, A.; Stoddart, L.A.; Hill, S.J.; Carlsson, J. Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models. J. Med. Chem. 2015, 58, 9578-9590. [CrossRef] [PubMed].
    • (2015) J. Med. Chem , vol.58 , pp. 9578-9590
    • Ranganathan, A.1    Stoddart, L.A.2    Hill, S.J.3    Carlsson, J.4
  • 102
    • 84887035754 scopus 로고    scopus 로고
    • Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor
    • [CrossRef] [PubMed]
    • Chen, D.; Ranganathan, A.; IJzerman, A.P.; Siegal, G.; Carlsson, J. Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A(2A) adenosine receptor. J. Chem. Inf. Model. 2013, 53, 2701-2714. [CrossRef] [PubMed].
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 2701-2714
    • Chen, D.1    Ranganathan, A.2    I'Jzerman, A.P.3    Siegal, G.4    Carlsson, J.5
  • 103
    • 84895811180 scopus 로고    scopus 로고
    • Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors
    • [CrossRef] [PubMed]
    • Vass, M.; Schmidt, E.; Horti, F.; Keseru, G.M. Virtual fragment screening on GPCRs: A case study on dopamine D3 and histamine H4 receptors. Eur. J. Med. Chem. 2014, 77, 38-46. [CrossRef] [PubMed].
    • (2014) Eur. J. Med. Chem. , vol.77 , pp. 38-46
    • Vass, M.1    Schmidt, E.2    Horti, F.3    Keseru, G.M.4
  • 104
    • 84978923182 scopus 로고    scopus 로고
    • In silico exploration of the conformational universe of GPCRs
    • [CrossRef] [PubMed]
    • Rodríguez-Espigares, I.; Kaczor, A.A.; Selent, J. In silico Exploration of the Conformational Universe of GPCRs. Mol. Inform. 2016, 35, 227-237. [CrossRef] [PubMed].
    • (2016) Mol. Inform , vol.35 , pp. 227-237
    • Rodríguez-Espigares, I.1    Kaczor, A.A.2    Selent, J.3
  • 105
    • 84888614101 scopus 로고    scopus 로고
    • The impact of molecular dynamics sampling on the performance of virtual screening against GPCRs
    • [CrossRef] [PubMed]
    • Tarcsay, A.; Paragi, G.; Vass, M.; Jójárt, B.; Bogár, F.; Keseru, G.M. The impact of molecular dynamics sampling on the performance of virtual screening against GPCRs. J. Chem. Inf. Model. 2013, 53, 2990-2999. [CrossRef] [PubMed].
    • (2013) J. Chem. Inf. Model , vol.53 , pp. 2990-2999
    • Tarcsay, A.1    Paragi, G.2    Vass, M.3    Jójárt, B.4    Bogár, F.5    Keseru, G.M.6
  • 106
    • 84890917722 scopus 로고    scopus 로고
    • Cloud-based simulations on google exacycle reveal ligand modulation of GPCR activation pathways
    • [CrossRef] [PubMed]
    • Kohlhoff, K.J.; Shukla, D.; Lawrenz, M.; Bowman, G.R.; Konerding, D.E.; Belov, D.; Altman, R.B.; Pande, V.S. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat. Chem. 2013, 6, 15-21. [CrossRef] [PubMed].
    • (2013) Nat. Chem. , vol.6 , pp. 15-21
    • Kohlhoff, K.J.1    Shukla, D.2    Lawrenz, M.3    Bowman, G.R.4    Konerding, D.E.5    Belov, D.6    Altman, R.B.7    Pande, V.S.8
  • 107
    • 77950823494 scopus 로고    scopus 로고
    • Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor
    • [CrossRef] [PubMed]
    • Bhattacharya, S.; Vaidehi, N. Computational mapping of the conformational transitions in agonist selective pathways of a G-protein coupled receptor. J. Am. Chem. Soc. 2010, 132, 5205-5214. [CrossRef] [PubMed].
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 5205-5214
    • Bhattacharya, S.1    Vaidehi, N.2
  • 108
    • 84905014930 scopus 로고    scopus 로고
    • Strategies for improved modeling of GPCR-drug complexes: Blind predictions of serotonin receptors bound to ergotamine
    • [CrossRef] [PubMed]
    • Rodríguez, D.; Ranganathan, A.; Carlsson, J. Strategies for improved modeling of GPCR-drug complexes: Blind predictions of serotonin receptors bound to ergotamine. J. Chem. Inf. Model. 2014, 54, 2004-2021. [CrossRef] [PubMed].
    • (2014) J. Chem. Inf. Model , vol.54 , pp. 2004-2021
    • Rodríguez, D.1    Ranganathan, A.2    Carlsson, J.3
  • 109
    • 84875807317 scopus 로고    scopus 로고
    • Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor
    • [CrossRef] [PubMed]
    • Weiss, D.R.; Ahn, S.; Sassano, M.F.; Kleist, A.; Zhu, X.; Strachan, R.; Roth, B.L.; Lefkowitz, R.J.; Shoichet, B.K. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem. Biol. 2013, 8, 1018-1026. [CrossRef] [PubMed].
    • (2013) ACS Chem. Biol , vol.8 , pp. 1018-1026
    • Weiss, D.R.1    Ahn, S.2    Sassano, M.F.3    Kleist, A.4    Zhu, X.5    Strachan, R.6    Roth, B.L.7    Lefkowitz, R.J.8    Shoichet, B.K.9
  • 110
    • 84925606909 scopus 로고    scopus 로고
    • Identifying modulators of CXC receptors 3 and 4 with tailored selectivity using multi-Target docking
    • [CrossRef] [PubMed]
    • Schmidt, D.; Bernat, V.; Brox, R.; Tschammer, N.; Kolb, P. Identifying modulators of CXC receptors 3 and 4 with tailored selectivity using multi-Target docking. ACS Chem. Biol. 2015, 10, 715-724. [CrossRef] [PubMed].
    • (2015) ACS Chem. Biol , vol.10 , pp. 715-724
    • Schmidt, D.1    Bernat, V.2    Brox, R.3    Tschammer, N.4    Kolb, P.5
  • 111
    • 84905730759 scopus 로고    scopus 로고
    • Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands
    • Rodríguez, D.; Brea, J.; Loza, M.I.; Carlsson, J. Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. Structure 2014, 22, 1140-1151.
    • (2014) Structure , vol.22 , pp. 1140-1151
    • Rodríguez, D.1    Brea, J.2    Loza, M.I.3    Carlsson, J.4
  • 112
    • 84988672537 scopus 로고    scopus 로고
    • Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor
    • [CrossRef] [PubMed]
    • Miao, Y.; Goldfeld, D.A.; Moo, E.V.; Sexton, P.M.; Christopoulos, A.; McCammon, J.A.; Valant, C. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor. Proc. Natl. Acad. Sci. USA 2016, 113, E5675-E5684. [CrossRef] [PubMed].
    • (2016) Proc. Natl. Acad. Sci. USA , vol.113 , pp. E5675-E5684
    • Miao, Y.1    Goldfeld, D.A.2    Moo, E.V.3    Sexton, P.M.4    Christopoulos, A.5    McCammon, J.A.6    Valant, C.7
  • 113
    • 84957310327 scopus 로고    scopus 로고
    • Novel scaffold identification of mglu1 receptor negative allosteric modulators using a hierarchical virtual screening approach
    • [CrossRef] [PubMed]
    • Jang, J.W.; Cho, N.-C.; Min, S.-J.; Cho, Y.S.; Park, K.D.; Seo, S.H.; No, K.T.; Pae, A.N. Novel Scaffold Identification of mGlu1 Receptor Negative Allosteric Modulators Using a Hierarchical Virtual Screening Approach. Chem. Biol. Drug Des. 2016, 87, 239-256. [CrossRef] [PubMed].
    • (2016) Chem. Biol. Drug Des. , vol.87 , pp. 239-256
    • Jang, J.W.1    Cho, N.-C.2    Min, S.-J.3    Cho, Y.S.4    Park, K.D.5    Seo, S.H.6    No, K.T.7    Pae, A.N.8
  • 115
    • 84878778709 scopus 로고    scopus 로고
    • Recent trends and future prospects in computational GPCR drug discovery: From virtual screening to polypharmacology
    • [CrossRef] [PubMed]
    • Carrieri, A.; Pérez-Nueno, V.I.; Lentini, G.; Ritchie, D.W. Recent trends and future prospects in computational GPCR drug discovery: From virtual screening to polypharmacology. Curr. Top. Med. Chem. 2013, 13, 1069-1097. [CrossRef] [PubMed].
    • (2013) Curr. Top. Med. Chem. , vol.13 , pp. 1069-1097
    • Carrieri, A.1    Pérez-Nueno, V.I.2    Lentini, G.3    Ritchie, D.W.4
  • 117
    • 84978842954 scopus 로고    scopus 로고
    • Revealing atomic-level mechanisms of protein allostery with molecular dynamics simulations
    • [CrossRef] [PubMed]
    • Hertig, S.; Latorraca, N.R.; Dror, R.O. Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations. PLoS Comput. Biol. 2016, 12, e1004746. [CrossRef] [PubMed].
    • (2016) Plos Comput. Biol. , vol.12 , pp. e1004746
    • Hertig, S.1    Latorraca, N.R.2    Dror, R.O.3
  • 119
    • 84863661333 scopus 로고    scopus 로고
    • Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules
    • [CrossRef] [PubMed]
    • Bakan, A.; Nevins, N.; Lakdawala, A.S.; Bahar, I. Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules. J. Chem. Theory Comput. 2012, 8, 2435-2447. [CrossRef] [PubMed].
    • (2012) J. Chem. Theory Comput , vol.8 , pp. 2435-2447
    • Bakan, A.1    Nevins, N.2    Lakdawala, A.S.3    Bahar, I.4
  • 120
    • 77955249382 scopus 로고    scopus 로고
    • Mapping the druggable allosteric space of G-protein coupled receptors: A fragment-based molecular dynamics approach
    • [CrossRef] [PubMed]
    • Ivetac, A.; McCammon, J.A. Mapping the druggable allosteric space of G-protein coupled receptors: A fragment-based molecular dynamics approach. Chem. Biol. Drug Des. 2010, 76, 201-217. [CrossRef] [PubMed].
    • (2010) Chem. Biol. Drug Des. , vol.76 , pp. 201-217
    • Ivetac, A.1    McCammon, J.A.2
  • 121
    • 84867010936 scopus 로고    scopus 로고
    • Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1
    • [CrossRef] [PubMed]
    • Tan, Y.S.; Sledz, P.; Lang, S.; Stubbs, C.J.; Spring, D.R.; Abell, C.; Best, R.B. Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1. Angew. Chem. 2012, 51, 10078-10081. [CrossRef] [PubMed].
    • (2012) Angew. Chem , vol.51 , pp. 10078-10081
    • Tan, Y.S.1    Sledz, P.2    Lang, S.3    Stubbs, C.J.4    Spring, D.R.5    Abell, C.6    Best, R.B.7
  • 122
    • 79960007037 scopus 로고    scopus 로고
    • Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
    • [CrossRef] [PubMed]
    • Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2011, 108, 10184-10189. [CrossRef] [PubMed].
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 126
    • 80052077522 scopus 로고    scopus 로고
    • Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
    • [CrossRef] [PubMed]
    • Johnston, J.M.; Filizola, M. Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors. Curr. Opin. Struct. Biol. 2011, 21, 552-558. [CrossRef] [PubMed].
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 552-558
    • Johnston, J.M.1    Filizola, M.2
  • 127
    • 77952921531 scopus 로고    scopus 로고
    • A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor
    • [CrossRef] [PubMed]
    • Hurst, D.P.; Grossfield, A.; Lynch, D.L.; Feller, S.; Romo, T.D.; Gawrisch, K.; Pitman, M.C.; Reggio, P.H. A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor. J. Biol. Chem. 2010, 285, 17954-17964. [CrossRef] [PubMed].
    • (2010) J. Biol. Chem. , vol.285 , pp. 17954-17964
    • Hurst, D.P.1    Grossfield, A.2    Lynch, D.L.3    Feller, S.4    Romo, T.D.5    Gawrisch, K.6    Pitman, M.C.7    Reggio, P.H.8
  • 130
    • 70350230389 scopus 로고    scopus 로고
    • Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics
    • [CrossRef] [PubMed]
    • Provasi, D.; Bortolato, A.; Filizola, M. Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics. Biochemistry (Mosc.) 2009, 48, 10020-10029. [CrossRef] [PubMed].
    • (2009) Biochemistry (Mosc.) , vol.48 , pp. 10020-10029
    • Provasi, D.1    Bortolato, A.2    Filizola, M.3
  • 131
    • 84894680958 scopus 로고    scopus 로고
    • Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale
    • [CrossRef] [PubMed]
    • Sabbadin, D.; Moro, S. Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale. J. Chem. Inf. Model. 2014, 54, 372-376. [CrossRef] [PubMed].
    • (2014) J. Chem. Inf. Model , vol.54 , pp. 372-376
    • Sabbadin, D.1    Moro, S.2
  • 132
    • 3142716857 scopus 로고    scopus 로고
    • Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
    • [CrossRef] [PubMed]
    • Hamelberg, D.; Mongan, J.; McCammon, J.A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120, 11919-11929. [CrossRef] [PubMed].
    • (2004) J. Chem. Phys. , vol.120 , pp. 11919-11929
    • Hamelberg, D.1    Mongan, J.2    McCammon, J.A.3
  • 133
    • 84997830677 scopus 로고    scopus 로고
    • How oliceridine (TRV-130) binds and stabilizes a μ-opioid receptor conformational state that selectively triggers g protein-signaling pathways
    • [CrossRef] [PubMed]
    • Schneider, S.; Provasi, D.; Filizola, M. How Oliceridine (TRV-130) Binds and Stabilizes a μ-Opioid Receptor Conformational State that Selectively Triggers G Protein-Signaling Pathways. Biochemistry (Mosc.) 2016. [CrossRef] [PubMed].
    • (2016) Biochemistry (Mosc.)
    • Schneider, S.1    Provasi, D.2    Filizola, M.3
  • 134
    • 84938914048 scopus 로고    scopus 로고
    • Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
    • [CrossRef] [PubMed]
    • Kappel, K.; Miao, Y.; McCammon, J.A. Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor. Q. Rev. Biophys. 2015, 48, 479-487. [CrossRef] [PubMed].
    • (2015) Q. Rev. Biophys , vol.48 , pp. 479-487
    • Kappel, K.1    Miao, Y.2    McCammon, J.A.3
  • 135
    • 84983360040 scopus 로고    scopus 로고
    • Cholesterol-dependent conformational plasticity in GPCR dimers
    • [CrossRef] [PubMed]
    • Prasanna, X.; Sengupta, D.; Chattopadhyay, A. Cholesterol-dependent Conformational Plasticity in GPCR Dimers. Sci. Rep. 2016, 6, 31858. [CrossRef] [PubMed].
    • (2016) Sci. Rep. , vol.6 , pp. 31858
    • Prasanna, X.1    Sengupta, D.2    Chattopadhyay, A.3
  • 136
    • 84999683667 scopus 로고    scopus 로고
    • Dynamic cholesterol-conditioned dimerization of the g protein coupled chemokine receptor type 4
    • [CrossRef] [PubMed]
    • Pluhackova, K.; Gahbauer, S.; Kranz, F.; Wassenaar, T.A.; Böckmann, R.A. Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4. PLoS Comput. Biol. 2016, 12, e1005169. [CrossRef] [PubMed].
    • (2016) PLoS Comput. Biol. , vol.12 , pp. e1005169
    • Pluhackova, K.1    Gahbauer, S.2    Kranz, F.3    Wassenaar, T.A.4    Böckmann, R.A.5
  • 137
    • 84947998906 scopus 로고    scopus 로고
    • Activation and allosteric modulation of human μ opioid receptor in molecular dynamics
    • [CrossRef] [PubMed]
    • Bartuzi, D.; Kaczor, A.A.; Matosiuk, D. Activation and allosteric modulation of human μ opioid receptor in molecular dynamics. J. Chem. Inf. Model. 2015, 55, 2421-2434. [CrossRef] [PubMed].
    • (2015) J. Chem. Inf. Model. , vol.55 , pp. 2421-2434
    • Bartuzi, D.1    Kaczor, A.A.2    Matosiuk, D.3
  • 139
    • 84978177103 scopus 로고    scopus 로고
    • Accelerated molecular dynamics simulations of the octopamine receptor using GPUS: Discovery of an alternate agonist-binding position
    • [CrossRef] [PubMed]
    • Kastner, K.W.; Izaguirre, J.A. Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: Discovery of an alternate agonist-binding position. Proteins 2016, 84, 1480-1489. [CrossRef] [PubMed].
    • (2016) Proteins , vol.84 , pp. 1480-1489
    • Kastner, K.W.1    Izaguirre, J.A.2
  • 140
    • 84997796763 scopus 로고    scopus 로고
    • Identification of two distinct sites for antagonist and biased agonist binding to the human chemokine receptor CXCR3
    • [CrossRef] [PubMed]
    • Milanos, L.; Saleh, N.; Kling, R.C.; Kaindl, J.; Tschammer, N.; Clark, T. Identification of Two Distinct Sites for Antagonist and Biased Agonist Binding to the Human Chemokine Receptor CXCR3. Angew. Chem. 2016, 55, 15277-15281. [CrossRef] [PubMed].
    • (2016) Angew. Chem. , vol.55 , pp. 15277-15281
    • Milanos, L.1    Saleh, N.2    Kling, R.C.3    Kaindl, J.4    Tschammer, N.5    Clark, T.6
  • 141
    • 85033440119 scopus 로고    scopus 로고
    • Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations
    • [CrossRef] [PubMed]
    • Okimoto, N.; Suenaga, A.; Taiji, M. Evaluation of protein-ligand affinity prediction using steered molecular dynamics simulations. J. Biomol. Struct. Dyn. 2016, 1-11. [CrossRef] [PubMed].
    • (2016) J. Biomol. Struct. Dyn , pp. 1-11
    • Okimoto, N.1    Suenaga, A.2    Taiji, M.3
  • 142
    • 84894684164 scopus 로고    scopus 로고
    • Steered molecular dynamics simulations for studying protein-ligand interaction in cyclin-dependent kinase 5
    • [CrossRef] [PubMed]
    • Patel, J.S.; Berteotti, A.; Ronsisvalle, S.; Rocchia, W.; Cavalli, A. Steered Molecular Dynamics Simulations for Studying Protein-Ligand Interaction in Cyclin-Dependent Kinase 5. J. Chem. Inf. Model. 2014, 54, 470-480. [CrossRef] [PubMed].
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 470-480
    • Patel, J.S.1    Berteotti, A.2    Ronsisvalle, S.3    Rocchia, W.4    Cavalli, A.5
  • 145
    • 0033947541 scopus 로고    scopus 로고
    • Functional significance of oligomerization of G-protein-coupled receptors
    • CrossRef
    • Salahpour, A.; Angers, S.; Bouvier, M. Functional significance of oligomerization of G-protein-coupled receptors. Trends Endocrinol. Metab. 2000, 11, 163-168. [CrossRef].
    • (2000) Trends Endocrinol. Metab , vol.11 , pp. 163-168
    • Salahpour, A.1    Angers, S.2    Bouvier, M.3
  • 146
    • 69249206623 scopus 로고    scopus 로고
    • G protein-coupled receptor hetero-dimerization: Contribution to pharmacology and function
    • [CrossRef] [PubMed]
    • Milligan, G. G protein-coupled receptor hetero-dimerization: Contribution to pharmacology and function. Br. J. Pharmacol. 2009, 158, 5-14. [CrossRef] [PubMed].
    • (2009) Br. J. Pharmacol. , vol.158 , pp. 5-14
    • Milligan, G.1
  • 147
    • 80053487319 scopus 로고    scopus 로고
    • Oligomerization of G protein-coupled receptors: Computational methods
    • [CrossRef] [PubMed]
    • Selent, J.; Kaczor, A.A. Oligomerization of G protein-coupled receptors: Computational methods. Curr. Med. Chem. 2011, 18, 4588-4605. [CrossRef] [PubMed].
    • (2011) Curr. Med. Chem. , vol.18 , pp. 4588-4605
    • Selent, J.1    Kaczor, A.A.2
  • 148
    • 80053511695 scopus 로고    scopus 로고
    • Oligomerization of G protein-coupled receptors: Biochemical and biophysical methods
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Selent, J. Oligomerization of G protein-coupled receptors: Biochemical and biophysical methods. Curr. Med. Chem. 2011, 18, 4606-4634. [CrossRef] [PubMed].
    • (2011) Curr. Med. Chem , vol.18 , pp. 4606-4634
    • Kaczor, A.A.1    Selent, J.2
  • 150
    • 84885903105 scopus 로고    scopus 로고
    • Simulating G protein-coupled receptors in native-like membranes: From monomers to oligomers
    • PubMed
    • Guixà-González, R.; Ramírez-Anguita, J.M.; Kaczor, A.A.; Selent, J. Simulating G protein-coupled receptors in native-like membranes: From monomers to oligomers. Methods Cell Biol. 2013, 117, 63-90. [PubMed].
    • (2013) Methods Cell Biol , vol.117 , pp. 63-90
    • Guixà-González, R.1    Ramírez-Anguita, J.M.2    Kaczor, A.A.3    Selent, J.4
  • 153
    • 84882454897 scopus 로고    scopus 로고
    • Modeling complexes of transmembrane proteins: Systematic analysis of protein-protein docking tools
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Selent, J.; Sanz, F.; Pastor, M. Modeling Complexes of Transmembrane Proteins: Systematic Analysis of Protein-Protein Docking Tools. Mol. Inform. 2013, 32, 717-733. [CrossRef] [PubMed].
    • (2013) Mol. Inform. , vol.32 , pp. 717-733
    • Kaczor, A.A.1    Selent, J.2    Sanz, F.3    Pastor, M.4
  • 154
    • 84885495867 scopus 로고    scopus 로고
    • An analysis of oligomerization interfaces in transmembrane proteins
    • [CrossRef] [PubMed]
    • Duarte, J.M.; Biyani, N.; Baskaran, K.; Capitani, G. An analysis of oligomerization interfaces in transmembrane proteins. BMC Struct. Biol. 2013, 13, 21. [CrossRef] [PubMed].
    • (2013) BMC Struct. Biol , vol.13 , pp. 21
    • Duarte, J.M.1    Biyani, N.2    Baskaran, K.3    Capitani, G.4
  • 157
    • 33750508943 scopus 로고    scopus 로고
    • Computational prediction of homodimerization of the A3 adenosine receptor
    • [CrossRef] [PubMed]
    • Kim, S.-K.; Jacobson, K.A. Computational prediction of homodimerization of the A3 adenosine receptor. J. Mol. Graph. Model. 2006, 25, 549-561. [CrossRef] [PubMed].
    • (2006) J. Mol. Graph. Model. , vol.25 , pp. 549-561
    • Kim, S.-K.1    Jacobson, K.A.2
  • 158
    • 0344875553 scopus 로고    scopus 로고
    • Adenosine A2A-dopamine D2 receptor-receptor heteromerization: Qualitative and quantitative assessment by fluorescence and bioluminescence energy transfer
    • [CrossRef] [PubMed]
    • Canals, M.; Marcellino, D.; Fanelli, F.; Ciruela, F.; de Benedetti, P.; Goldberg, S.R.; Neve, K.; Fuxe, K.; Agnati, L.F.; Woods, A.S.; et al. Adenosine A2A-dopamine D2 receptor-receptor heteromerization: Qualitative and quantitative assessment by fluorescence and bioluminescence energy transfer. J. Biol. Chem. 2003, 278, 46741-46749. [CrossRef] [PubMed].
    • (2003) J. Biol. Chem. , vol.278 , pp. 46741-46749
    • Canals, M.1    Marcellino, D.2    Fanelli, F.3    Ciruela, F.4    De Benedetti, P.5    Goldberg, S.R.6    Neve, K.7    Fuxe, K.8    Agnati, L.F.9    Woods, A.S.10
  • 159
    • 67349220011 scopus 로고    scopus 로고
    • Computational study of the heterodimerization between mu and delta receptors
    • [CrossRef] [PubMed]
    • Liu, X.; Kai, M.; Jin, L.; Wang, R. Computational study of the heterodimerization between mu and delta receptors. J. Comput. Aided Mol. Des. 2009, 23, 321-332. [CrossRef] [PubMed].
    • (2009) J. Comput. Aided Mol. des , vol.23 , pp. 321-332
    • Liu, X.1    Kai, M.2    Jin, L.3    Wang, R.4
  • 160
    • 67650089750 scopus 로고    scopus 로고
    • Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions
    • [CrossRef] [PubMed]
    • Bruno, A.; Guadix, A.E.; Costantino, G. Molecular dynamics simulation of the heterodimeric mGluR2/5HT(2A) complex. An atomistic resolution study of a potential new target in psychiatric conditions. J. Chem. Inf. Model. 2009, 49, 1602-1616. [CrossRef] [PubMed].
    • (2009) J. Chem. Inf. Model , vol.49 , pp. 1602-1616
    • Bruno, A.1    Guadix, A.E.2    Costantino, G.3
  • 161
    • 84926467217 scopus 로고    scopus 로고
    • Multi-component protein-protein docking based protocol with external scoring for modeling dimers of g protein-coupled receptors
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Guixà-González, R.; Carrió, P.; Poso, A.; Dove, S.; Pastor, M.; Selent, J. Multi-Component Protein-Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors. Mol. Inform. 2015, 34, 246-255. [CrossRef] [PubMed].
    • (2015) Mol. Inform. , vol.34 , pp. 246-255
    • Kaczor, A.A.1    Guixà-González, R.2    Carrió, P.3    Poso, A.4    Dove, S.5    Pastor, M.6    Selent, J.7
  • 162
    • 84867576743 scopus 로고    scopus 로고
    • Fractal dimension as a measure of surface roughness of G protein-coupled receptors: Implications for structure and function
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Guixà-González, R.; Carrió, P.; Obiol-Pardo, C.; Pastor, M.; Selent, J. Fractal dimension as a measure of surface roughness of G protein-coupled receptors: Implications for structure and function. J. Mol. Model. 2012, 18, 4465-4475. [CrossRef] [PubMed].
    • (2012) J. Mol. Model. , vol.18 , pp. 4465-4475
    • Kaczor, A.A.1    Guixà-González, R.2    Carrió, P.3    Obiol-Pardo, C.4    Pastor, M.5    Selent, J.6
  • 163
    • 84982811760 scopus 로고    scopus 로고
    • The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: Homology modeling, docking and molecular dynamics
    • [CrossRef] [PubMed]
    • Kaczor, A.A.; Jörg, M.; Capuano, B. The dopamine D2 receptor dimer and its interaction with homobivalent antagonists: Homology modeling, docking and molecular dynamics. J. Mol. Model. 2016, 22, 203. [CrossRef] [PubMed].
    • (2016) J. Mol. Model. , vol.22 , pp. 203
    • Kaczor, A.A.1    Jörg, M.2    Capuano, B.3
  • 164
    • 84903287603 scopus 로고    scopus 로고
    • Investigation of novel ropinirole analogues: Synthesis, pharmacological evaluation and computational analysis of dopamine D2 receptor functionalized congeners and homobivalent ligands
    • CrossRef
    • Jorg, M.; Kaczor, A.A.; Mak, F.S.; Lee, K.C.K.; Poso, A.; Miller, N.D.; Scammells, P.J.; Capuano, B. Investigation of novel ropinirole analogues: Synthesis, pharmacological evaluation and computational analysis of dopamine D2 receptor functionalized congeners and homobivalent ligands. Med Chem Comm 2014, 5, 891-898. [CrossRef].
    • (2014) Med Chem Comm , vol.5 , pp. 891-898
    • Jorg, M.1    Kaczor, A.A.2    Mak, F.S.3    Lee, K.C.K.4    Poso, A.5    Miller, N.D.6    Scammells, P.J.7    Capuano, B.8
  • 165
    • 84962246245 scopus 로고    scopus 로고
    • GPU Accelerated molecular docking simulation with genetic algorithms
    • Squillero, G. Burelli, P. Eds. Lecture Notes in Computer Science; Springer International Publishing: Cham, Switzerland
    • Altuntas, S.; Bozkus, Z.; Fraguela, B.B. GPU Accelerated Molecular Docking Simulation with Genetic Algorithms. In Applications of Evolutionary Computation; Squillero, G., Burelli, P., Eds.; Lecture Notes in Computer Science; Springer International Publishing: Cham, Switzerland, 2016; pp. 134-146.
    • (2016) Applications of Evolutionary Computation , pp. 134-146
    • Altuntas, S.1    Bozkus, Z.2    Fraguela, B.B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.