1. Fanelli, F, De Benedetti, PG. Computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev. 2005;105:3297-3351. doi:10.1021/cr000095n.
Google Scholar | Crossref | Medline2. Palczewski, K, Kumasaka, T, Hori, T, et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science. 2000;289:739-745. doi:10.1126/science.289.5480.739.
Google Scholar | Crossref | Medline | ISI3. Stenkamp, RE, Filipek, S, Driessen, CA, Teller, DC, Palczewski, K. Crystal structure of rhodopsin: a template for cone visual pigments and other G protein-coupled receptors. Biochim Biophys Acta. 2002;1565:168-182. doi:10.1016/s0005-2736(02)00567-9.
Google Scholar | Crossref | Medline4. Teller, DC, Okada, T, Behnke, CA, Palczewski, K, Stenkamp, RE. Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry. 2001;40:7761-7772. doi:10.1021/bi0155091.
Google Scholar | Crossref | Medline5. Okada, T, Fujiyoshi, Y, Silow, M, Navarro, J, Landau, EM, Shichida, Y. Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc Natl Acad Sci USA. 2002;99:5982-5987. doi:10.1073/pnas.082666399.
Google Scholar | Crossref | Medline6. Cherezov, V, Rosenbaum, DM, Hanson, MA, et al. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science. 2007;318:1258-1265. doi:10.1126/science.1150577.
Google Scholar | Crossref | Medline | ISI7. Chai, JT, Digby, JE, Choudhury, RP. GPR109A and vascular inflammation. Curr Atheroscler Rep. 2013;15:325. doi:10.1007/s11883-013-0325-9.
Google Scholar | Crossref | Medline8. Shi, Y, Lai, X, Ye, L, et al. Activated niacin receptor HCA2 inhibits chemoattractant-mediated macrophage migration via Gbetagamma/PKC/ERK1/2 pathway and heterologous receptor desensitization. Sci Rep. 2017;7:42279. doi:10.1038/srep42279.
Google Scholar | Crossref | Medline9. Soga, T, Kamohara, M, Takasaki, J, et al. Molecular identification of nicotinic acid receptor. Biochem Biophys Res Commun. 2003;303:364-369. doi:10.1016/s0006-291x(03)00342-5.
Google Scholar | Crossref | Medline | ISI10. Tunaru, S, Kero, J, Schaub, A, et al. PUMA-G and HM74 are receptors for nicotinic acid and mediate its anti-lipolytic effect. Nat Med. 2003;9:352-355. doi:10.1038/nm824.
Google Scholar | Crossref | Medline11. Wise, A, Foord, SM, Fraser, NJ, et al. Molecular identification of high and low affinity receptors for nicotinic acid. J Biol Chem. 2003;278:9869-9874. doi:10.1074/jbc.M210695200.
Google Scholar | Crossref | Medline | ISI12. Shen, HC, Ding, FX, Luell, S, et al. Discovery of biaryl anthranilides as full agonists for the high affinity niacin receptor. J Med Chem. 2007;50:6303-6306. doi:10.1021/jm700942d.
Google Scholar | Crossref | Medline13. Shen, HC, Szymonifka, MJ, Kharbanda, D, et al. Discovery of orally bioavailable and novel urea agonists of the high affinity niacin receptor GPR109A. Bioorg Med Chem Lett. 2007;17:6723-6728. doi:10.1016/j.bmcl.2007.10.055.
Google Scholar | Crossref | Medline14. Olsson, AG . Nicotinic acid and derivatives. In: Schettler, G, Habenicht, AJR, eds. Principles and Treatment of Lipoprotein Disorders Handbook of Experimental Pharmacology. Vol. 109. Berlin: Springer; 1994:349-400. doi:10.1007/978-3-642-78426-2_13.
Google Scholar | Crossref15. Shi, L, Javitch, JA. The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice. Proc Natl Acad Sci USA. 2004;101:440-445. doi:10.1073/pnas.2237265100.
Google Scholar | Crossref | Medline16. Zhao, MM, Hwa, J, Perez, DM. Identification of critical extracellular loop residues involved in alpha 1-adrenergic receptor subtype-selective antagonist binding. Mol Pharmacol. 1996;50:1118-1126.
Google Scholar | Medline17. Kim, J, Jiang, Q, Glashofer, M, Yehle, S, Wess, J, Jacobson, KA. Glutamate residues in the second extracellular loop of the human A2a adenosine receptor are required for ligand recognition. Mol Pharmacol. 1996;49:683-691.
Google Scholar | Medline18. Kristiansen, K. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function. Pharmacol Ther. 2004;103:21-80. doi:10.1016/j.pharmthera.2004.05.002.
Google Scholar | Crossref | Medline | ISI19. Shi, L, Javitch, JA. The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol. 2002;42:437-467. doi:10.1146/annurev.pharmtox.42.091101.144224.
Google Scholar | Crossref | Medline20. Bonini, JA, Jones, KA, Adham, N, et al. Identification and characterization of two G protein-coupled receptors for neuropeptide FF. J Biol Chem. 2000;275:39324-39331. doi:10.1074/jbc.M004385200.
Google Scholar | Crossref | Medline | ISI21. Ji, TH, Grossmann, M, Ji, I. G protein-coupled receptors. I. Diversity of receptor-ligand interactions. J Biol Chem. 1998;273:17299-17302. doi:10.1074/jbc.273.28.17299.
Google Scholar | Crossref | Medline | ISI22. Strader, CD, Fong, TM, Tota, MR, Underwood, D, Dixon, RA. Structure and function of G protein-coupled receptors. Annu Rev Biochem. 1994;63:101-132. doi:10.1146/annurev.bi.63.070194.000533.
Google Scholar | Crossref | Medline | ISI23. Tunaru, S, Lattig, J, Kero, J, Krause, G, Offermanns, S. Characterization of determinants of ligand binding to the nicotinic acid receptor GPR109A (HM74A/PUMA-G). Mol Pharmacol. 2005;68:1271-1280. doi:10.1124/mol.105.015750.
Google Scholar | Crossref | Medline | ISI24. Salomon-Ferrer, R, Gotz, AW, Poole, D, Le Grand, S, Walker, RC. Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald. J Chem Theory Comput. 2013;9:3878-3888. doi:10.1021/ct400314y.
Google Scholar | Crossref | Medline25. Brooks, BR, Brooks, CL, Mackerell, AD, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30:1545-1614. doi:10.1002/jcc.21287.
Google Scholar | Crossref | Medline | ISI26. Phillips, JC, Hardy, DJ, Maia, JDC, et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J Chem Phys. 2020;153:044130. doi:10.1063/5.0014475.
Google Scholar | Crossref | Medline27. Van Der Spoel, D, Lindahl, E, Hess, B, Groenhof, G, Mark, AE, Berendsen, HJ. GROMACS: fast, flexible, and free. J Comput Chem. 2005;26:1701-1718. doi:10.1002/jcc.20291.
Google Scholar | Crossref | Medline | ISI28. Dror, RO, Pan, AC, Arlow, DH, et al. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci USA. 2011;108:13118-13123. doi:10.1073/pnas.1104614108.
Google Scholar | Crossref | Medline29. Zhang, J, Yang, J, Jang, R, Zhang, Y. GPCR-I-TASSER: a hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure. 2015;23:1538-1549. doi:10.1016/j.str.2015.06.007.
Google Scholar | Crossref | Medline30. Kelley, LA, Mezulis, S, Yates, CM, Wass, MN, Sternberg, MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015;10:845-858. doi:10.1038/nprot.2015.053.
Google Scholar | Crossref | Medline | ISI31. Waterhouse, A, Bertoni, M, Bienert, S, et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 2018;46:W296-W303. doi:10.1093/nar/gky427.
Google Scholar | Crossref | Medline32. Soding, J, Biegert, A, Lupas, AN. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005;33:W244-W248. doi:10.1093/nar/gki408.
Google Scholar | Crossref33. Webb, B, Sali, A. Comparative protein structure modeling using MODELLER. Curr Protoc Bioinformatics. 2016;54:5.6.1-5.6.37. doi:10.1002/cpbi.3.
Google Scholar | Crossref | Medline34. Sali, A, Blundell, TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993;234:779-815. doi:10.1006/jmbi.1993.1626.
Google Scholar | Crossref | Medline | ISI35. Fiser, A, Do, RK, Sali, A. Modeling of loops in protein structures. Protein Sci. 2000;9:1753-1773. doi:10.1110/ps.9.9.1753.
Google Scholar | Crossref | Medline | ISI36. Olsson, MH, Sondergaard, CR, Rostkowski, M, Jensen, JH. PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions. J Chem Theory Comput. 2011;7:525-537. doi:10.1021/ct100578z.
Google Scholar | Crossref | Medline37. Laskowski, RA, MacArthur, MW, Moss, DS, Thornton, JM. PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst. 1993;26:283-291. doi:10.1107/S0021889892009944.
Google Scholar | Crossref | ISI38. Colovos, C, Yeates, TO. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci. 1993;2:1511-1519. doi:10.1002/pro.5560020916.
Google Scholar | Crossref | Medline | ISI39. Morris, GM, Huey, R, Lindstrom, W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30:2785-2791. doi:10.1002/jcc.21256.
Google Scholar | Crossref | Medline | ISI40. Chintapalli, SV, Bhardwaj, G, Patel, R, et al. Molecular dynamic simulations reveal the structural determinants of Fatty Acid binding to oxy-myoglobin. PLoS ONE. 2015;10:e0128496. doi:10.1371/journal.pone.0128496.
Google Scholar | Crossref | Medline41. Chintapalli, SV, Jayanthi, S, Mallipeddi, PL, et al. Novel molecular interactions of acylcarnitines and fatty acids with myoglobin. J Biol Chem. 2016;291:25133-25143. doi:10.1074/jbc.M116.754978.
Google Scholar | Crossref | Medline42. Humphrey, W, Dalke, A, Schulten, K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33-827. doi:10.1016/0263-7855(96)00018-5.
Google Scholar | Crossref | Medline43. MacKerell, AD, Bashford, D, Bellott, M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102:3586-3616. doi:10.1021/jp973084f.
Google Scholar | Crossref | Medline | ISI