1. F. Felline, M Seeber, F. Fanelli (2022) PSNtools for standalone and web-based structure network analyses of conformational ensembles. Comput. Struct. Biotechnol. J. 20: 640-649.
  2. A Felline, D Schiroli, A Comitato, V Marigo, F. Fanelli (2021) Structure network-based landscape of rhodopsin misfolding by mutations and algorithmic prediction of small chaperone action. Comput. Struct. Biotechnol. J. 19: 6020-6038.
  3. F. Fanelli, A Felline, V Marigo (2021) Structural aspects of rod opsin and their implication in genetic diseases Pflügers Archiv-European Journal of Physiology 473: 1339-1359.
  4. M.‐A. Mroginski, S. Adam, G. S Amoyal, A. Barnoy, A.‐N. Bondar, V. A Borin, J. R Church, T. Domratcheva, B. Ensing, F. Fanelli, N. Ferré, O. Filiba, L. Pedraza‐González, R. González, C. Gonzalez Espinoza, R. K Kar, L. Kemmler, Seung S. Kim, J.b Kongsted, A. I Krylov, Y. Lahav, M. Lazaratos, Q. NasserEddin, I. Navizet, A. N., M. Olivucci, J. Magnus Haugaard Olsen, A. Pérez de Alba Ortíz, E. Pieri, A. G Rao, Y. Min Rhee, N. Ricardi, S. Sen, I. A Solov’yov, L. De Vico, T. Adam Wesolowski, C. Wiebeler, X. Yang, I. Schapiro (2021) Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology 97: 243-269.
  5. L. Casarini, C. Lazzaretti, E. Paradiso, S. Limoncella, L. Riccetti, S. Sperduti, B. Melli, S. Marcozzi, C. Anzivino, N. S. Sayers, J. Czapinski, G. Brigante, F. Poti, Antonio La Marca, F. De Pascali, E. Reiter, A. Falbo, J. Daolio, M. T. Villani, M. Lispi, G. Orlando, F. G. Klinger, F. Fanelli, A. R.-Muller, A. C. Hanyaloglu, M. Simoni. (2020) Membrane estrogen receptor (GPER) and follicle-stimulating hormone receptor (FSHR) heteromeric complexes promote human ovarian follicle survival. iScience 23: 101812.
  6. D. Fontana, M. Mauri, R. Renso, M. Docci, I. Crespiatico, L. M. Røst, M. Jang, A. Niro, D. D’Aliberti, L. Massimino, M. Bertagna, G. Zambrotta, M. Bossi, S. Citterio, B. Crescenzi, F. Fanelli, V. Cassina, R. Corti, D. Salerno, L. Nardo, C. Chinello, F. Mantegazza, C. Mecucci, F. Magni, G. Cavaletti, P. Bruheim, D. Rea, S. Larsen, C. Gambacorti-Passerini & R. Piazza (2020) ETNK1 mutations induce a mutator phenotype that can be reverted with phosphoethanolamine. Nature Communications 11: 1-16.
  7. L Bellucci, A Felline, F. Fanelli (2020) Dynamics and structural communication in the ternary complex of fully phosphorylated V2 vasopressin receptor, vasopressin, and β-arrestin 1 BBA-Biomembranes 1862: 183355.
  8. A Felline, M Seeber, F. Fanelli (2020) webPSN v2. 0: a webserver to infer fingerprints of structural communication in biomacromolecules. Nucleic Acids Research 48: W94-W103.
  9. F. Fanelli, AC Hanyaloglu, K Jonas (2020) Integrated structural modeling and super-resolution imaging resolve GPCR oligomers Progress in molecular biology and translational science 169: 151-179.
  10. F Monacelli, L Martella, MN Parodi, P Odetti, F. Fanelli, M Tabaton (2019) Frontal Variant of Alzheimer’s Disease: A Report of a Novel PSEN1 Mutation. Journal of Alzheimer’s Disease 70: 11-15.
  11. A Felline, L Belmonte, F Raimondi, L Bellucci, F. Fanelli (2019) Interconnecting flexibility, structural communication, and function in RhoGEF oncoproteins J. Chem. Inf. Model. 59: 4300-4313.
  12. L. Pedraza-González, L. De Vico, M. del Carmen Marín, F. Fanelli, M. Olivucci (2019) ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counter-ion Placement (2019) J. Chem. Theory Comput. 15: 3134-3152.
  13. A. Subramanian, A. Capalbo, N.R. Iyengar, R. Rizzo, A. di Campli, R. Di Martino,M. Lo Monte, A.R. Beccari, A. Yerudkar, C. del Vecchio, L. Glielmo, G. Turacchio, M. Pirozzi, S.G. Kim, P. Henklein, J. Cancino, S. Parashuraman, D. Diviani, F. Fanelli, M. Sallese, A. Luini (2019). Auto-regulation of Secretory Flux by Sensing and Responding to the Folded Cargo Protein Load in the Endoplasmic Reticulum. Cell 176: 1461-1476.
  14. P.G. De Benedetti, F. Fanelli (2018) Computational modeling approaches to quantitative structure-binding kinetics relationships in drug discovery. Drug Discov. Today 23: 1396-1406.
  15. P. Behnen, A. Felline, A. Comitato, M. T. Di Salvo, F. Raimondi, S. Gulati, S. Kahremany, K. Palczewski, V. Marigo, F. Fanelli (2018) A Small Chaperone Improves Folding and Routing of Rhodopsin Mutants Linked to Inherited Blindness. iScience 4: 1-19.
  16. A. Felline, M. Ghitti, G. Musco, F. Fanelli (2017). Dissecting intrinsic and ligand-induced structural communication in the β3 headpiece of integrins. Biochimica et Biophysica Acta – General Subjects 1861: 2367-2381.
  17. J. Zapata, E. Moretto, S. Hannan, L. Murru, A. Longatti, D. Mazza, L. Benedetti, M. Fossati, C. Heise, L. Ponzoni, P. Valnegri, D. Braida, M. Sala, M. Francolini, J. Hildebrand, V. Kalscheuer, F. Fanelli, C. Sala, B. Bettler, S. Bassani, T.G. Smart, M. Passafaro (2017). Epilepsy and intellectual disability linked protein Shrm4 interaction with GABABRs shapes inhibitory neurotransmission. Nature Communications 8: 14536.
  18. A. Felline, S. Mariani, F. Raimondi, L. Bellucci, F. Fanelli (2017). Structural Determinants of Constitutive Activation of Gα Proteins: Transducin as a Paradigm. J. Chem. Theory Comput. 13: 886-899.
  19. F. Fanelli, A. Felline (2017) Uncovering GPCR and G Protein Function by Protein Structure Network Analysis. In Computational Tools for Chemical Biology (Martin-Santamaria, S. Ed), Book series Chemical Biology (Series Eds. K. J. Weissman, S. Flitsch, N.J. Westood) The Royal Society of Chemistry Cambridge UK, N. 3, 198-220.
  20. F. Fanelli, A. Felline (2017) Uncovering GPCR and G Protein Function by Protein Structure Network Analysis. In Computational Tools for Chemical Biology (Martin-Santamaria, S. Ed), Book series Chemical Biology (Series Eds. K. J. Weissman, S. Flitsch, N.J. Westood) The Royal Society of Chemistry Cambridge UK, N. 3, 198-220.
  21. A. C. Hanyaloglu, F. Fanelli, K. C. Jonas (2017) Class A GPCR: Di/Oligomerization of Glycoprotein Hormone Receptors in G-Protein-Coupled Receptor Dimers (K. Herrick-Davis, G. Milligan, G. Di Giovanni Eds) book series The Receptors (series Ed. G. Di Giovanni) Humana Press Springer International, Cham Switzerlansd, 207-232.
  22. H.L. Luk, N. Bhattacharyya, F. Montisci, J.M. Morrow, F. Melaccio, A. Wada, M. Sheves, F. Fanelli, B.S.W. Chang, M. Olivucci (2016). Modulation of thermal noise and spectral sensitivity in Lake Baikal cottoid fish rhodopsins. Sci. Reports 6: 38425.
  23. D. Diviani, F. Raimondi, C.D. Del Vescovo, E. Dreyer, E. Reggi, H. Osman, L. Ruggieri, C. Gonano, S. Cavin, C.L. Box, M. Lenoir, M. Overduin, L. Bellucci, M. Seeber, F. Fanelli (2016). Small-Molecule Protein-Protein Interaction Inhibitor of Oncogenic Rho Signaling. Cell Chem. Biol. 23: 1135-1146.
  24. F. Fanelli, A. Felline, F. Raimondi, M. Seeber (2016). Structure network analysis to gain insights into GPCR function. Biochem. Soc. Trans. 44:613-618.
  25. F. Raimondi, A. Felline, F. Fanelli (2015). Catching Functional Modes and Structural Communication in Dbl Family Rho Guanine Nucleotide Exchange Factors. J. Chem. Inf. Model. 55: 1878-1893.
  26. M.L. Mignogna, M. Giannandrea, A. Gurgone, F. Fanelli, F. Raimondi, L. Mapelli, S. Bassani, H. Fang, E. Van Anken, M. Alessio, M. Passafaro, S. Gatti, J.A. Esteban, R. Huganir, P. D’Adamo (2015). The intellectual disability protein RAB39B selectively regulates GluA2 trafficking to determine synaptic AMPAR composition. Nature Communications 6: 6504.
  27. K. C. Jonas, F. Fanelli, I. Huhtaniemi, A. Hanyaloglu (2015). Single Molecule Analysis of Functionally Asymmetric GPCR Oligomers reveals Diverse Spatial and Structural Assemblies. J. Biol. Chem. 290: 3875-3892.
  28. M. Seeber, A. Felline, F. Raimondi, S. Mariani, F. Fanelli (2015). WebPSN: a web server for high throughput investigation of structural communication in bio-macromolecules. Bioinformatics 31: 779-781.
  29. P. G. De Benedetti, F. Fanelli (2014). Multiscale quantum chemical approaches to QSAR modeling and drug design. Drug Discov. Today 19: 1921-1927.
  30. Rinaldi, F. Melaccio, S. Gozem, F. Fanelli, M. Olivucci (2014). Comparison of the isomerization mechanisms of human melanopsin and invertebrate and vertebrate rhodopsins. Proc. Natl. Acad. Sci. U S A 111: 1714-1719.
  31. S. Mariani, D. Dell’Orco, A. Felline, F. Raimondi, F. Fanelli (2013). Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases. PLoS Comput. Biol. 9: e1003207.
  32. F. Raimondi, A. Felline, M. Seeber, S. Mariani, F. Fanelli (2013). A mixed Protein Structure Network and Elastic Network Model approach to predict the structural communication in biomolecular systems. J. Chem. Theory Comput. 9: 2504-2518.
  33. E. Gracia, D. Farré, A. Cortés, C. Ferrer-Costa, M. Orozco, J. Mallol, C. Lluís, E. I. Canela, P. J. McCormick, R. Franco, F. Fanelli, V. Casadó (2013). The catalytic site structural gate of adenosine deaminase allosterically modulates ligand binding to adenosine receptors. FASEB J. 27: 1048-1061.
  34. F. Fanelli, F. Raimondi (2013). Nucleotide binding affects intrinsic dynamics and structural communication in Ras GTPases. Curr. Pharm. Des. 19: 4214-4225.
  35. F. Raimondi, A. Felline, G. Portella, M. Orozco, F. Fanelli (2013). Light on the structural communication in Ras GTPases. J. Biomol. Struct. Dyn. 31: 142-157.
  36. F. Fanelli, A. Felline, F. Raimondi (2013). Network analysis to uncover the structural communication in GPCRs. Methods Cell. Biol. 117: 43-61.
  37. F. Fanelli, M. Seeber, A. Felline, D. Casciari, F. Raimondi (2013). Quaternary structure predictions and structural communication features of GPCR dimers. Prog. Mol. Biol. Transl. Sci. 117:105-142.
  38. M. Giannotta, C. Ruggiero, M. Grossi, J. Cancino, M. Capitani, T. Pulvirenti, G.M. Consoli, C. Geraci, F. Fanelli, A. Luini, M. Sallese (2012). The KDEL receptor couples to Galpha(q/11) to activate Src kinases and regulate transport through the Golgi. The EMBO J 31: 2869-2881.
  39. F. Fanelli (2012). Modeling the structural communication in supramolecular complexes involving GPCRs. Meth. Mol. Biol. 914:319-336.
  40. F. Fanelli, P.G. De Benedetti (2011). Update 1 of Computational Modeling Approaches to Structure-Function Analysis of G Protein-Coupled Receptors. Chem. Rev., 111: PR438-535.
  41. G. DeMars, F. Fanelli, D. Puett (2011). The extreme C-terminal region of Galphas differentially couples to the luteinizing hormone and β2-adrenergic receptors. Mol. Endocrinol. 25: 1416-1430.
  42. F. Fanelli, M. Mauri, V. Capra, F. Raimondi, F. Guzzi, M. Ambrosio, G.E. Rovati, M. Parenti (2011). Light on the structure of thromboxane A2 receptor hetero-dimers Cell. Mol. Life Sci. 68: 3109-3120.
  43. F. Raimondi, G. Portella, M. Orozco, F. Fanelli (2011). Nucleotide binding switches the information flow in ras GTPases. PLoS Comput. Biol. 7: e1001098.
  44. F. Fanelli, A. Felline (2011). Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor. Biochim. Biophys. Acta 1808: 1256-1266.
  45. K. Angelova, A. Felline, M. Lee, M. Patel, D. Puett, F. Fanelli (2011). Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor. Cell. Mol. Life Sci. 68: 1227-1239.
  46. M. Seeber, A. Felline, F. Raimondi, S. Muff, R. Friedman, F. Rao, A. Caflisch and F. Fanelli (2011). Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J. Comput. Chem. 32: 1183-1194.
  47. P.G. De Benedetti, F. Fanelli (2010). Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR. Drug Discov. Today 15: 859-866.
  48. D. Puett, K. Angelova, M.R. da Costa, S.W. Warrenfeltz, F. Fanelli (2010). The luteinizing hormone receptor: insights into structure-function relationships and hormone-receptor-mediated changes in gene expression in ovarian cancer cells. Mol. Cell. Endocrinol. 329: 47-55.
  49. Carrieri, A. Piergentili, F. Del Bello, M. Giannella, M. Pigini, A. Leonardi, F. Fanelli, W. Quaglia (2010). Structure-activity relationships in 1,4-benzodioxan-related compounds. 10. Novel alpha1-adrenoreceptor antagonists related to openphendioxan: synthesis, biological evaluation, and alpha1d computational study. Bioorg. Med. Chem. 18: 7065-7077.
  50. M. Ambrosio, F. Fanelli, S. Brocchetti, F. Raimondi, M. Mauri, G.E. Rovati, V. Capra (2010). Superactive mutants of thromboxane prostanoid receptor: functional and computational analysis of an active form alternative to constitutively active mutants. Cell. Mol. Life Sci. 67: 2979-2989.
  51. F. Fanelli, M. Seeber (2010). Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants. FASEB J. 24: 3196-3209.
  52. F. Raimondi, M. Orozco, F. Fanelli (2010). Deciphering the deformation modes associated with function retention and specialization in members of the Ras Superfamily. Structure 18: 402-414.
  53. Soriano, R.Ventura, A. Molero, R. Hoen, V. Casadó, A. Cortés, F. Fanelli, F. Albericio, C. Lluís, R. Franco, M. Royo (2009). Adenosine A2A receptor-antagonist/Dopamine D2 receptor-agonist bivalent ligands as pharmacological tools to detect A2A-D2 receptor heteromers. J. Med. Chem. 52: 5590-5602.
  54. A. Felline, M. Seeber, F. Rao, F. Fanelli (2009). Computational screening of rhodopsin mutations associated with Retinitis Pigmentosa. J. Chem. Theory Comput. 5: 2472-2485.
  55. D. Dell’Orco, H. Schmidt, S. Mariani, F. Fanelli (2009). Network level analysis of light adaptation in rod cells under normal and altered conditions. Mol. BioSyst. 5: 1232-1246.
  56. P.G. De Benedetti, F. Fanelli (2009). Ligand-target communication and drug design. Curr. Protein Pept. Sci. 10: 186-193.
  57. F. Fanelli, P.G. De Benedetti, F. Raimondi, M. Seeber (2009). Computational modeling of intra and intermolecular communication in GPCRs. Curr. Prot. Pept. Sci. 10: 173-185.
  58. P Cozzini, G.E. Kellogg, F. Spyrakis, D.J. Abraham, G. Costantino, A. Emerson, F. Fanelli, H. Gohlke, L.A. Kuhn, G.M. Morris, M. Orozco, T.A. Pertinhez, M. Rizzi, C. Sotriffer (2008). Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J. Med. Chem. 51: 6237-6255.
  59. C. Casciari, D. Dell’Orco, F. Fanelli (2008). Homo-dimerization of neurotensin 1 receptor involves helices 1, 2 and 4: insights from quaternary structure predictions and dimerization free energy estimations. J. Chem. Inf. Mod. 48: 1669-1678.
  60. D. Dell’Orco, C. Casciari, F. Fanelli (2008). Quaternary structure predictions and estimation of mutational effects on the free energy of dimerization of the OMPLA protein. J. Struct. Biol. 163: 155-162.
  61. F. Fanelli, D. Dell’Orco (2008). Dark and photoactivated rhodopsin share common binding modes to transducin. FEBS Lett. 582: 991-996.
  62. F. Raimondi, M. Seeber, P.G. De Benedetti, F. Fanelli (2008). Mechanisms of inter- and intramolecular communication in GPCRs and G proteins. J. Am. Chem. Soc. 130: 4310-4325.
  63. X. Feng, T. Muller, D. Mizrachi, F. Fanelli, D.L. Segaloff (2008). An Intracellular Loop (IL2) Residue Confers Different Basal Constitutive Activities to the Human Lutropin Receptor and Human Thyrotropin Receptor through Structural Communication between IL2 and Helix 6, via Helix 3. Endocrinology 149: 1705-1717.
  64. K. Angelova, F. Fanelli, D. Puett (2008). Contributions of intracellular loops 2 and 3 of the lutropin receptor in Gs coupling. Mol. Endocrinol. 22: 126-38.
  65. F. Fanelli, P.G. De Benedetti (2008). Computational modeling of selective pharmacophores at the α1-adrenergic receptors. In Methods and Principles in Medicinal Chemistry (R. Mannhold, H. Kubinyi and G. Folkers Eds) Vol. 38 Antitargets: prediction and prevention of drug side effects (R. J. Vaz and T. Klabunde Editors.), WILEY-VCH Verlag, 155-193.
  66. M. Zhang, Y.X. Tao, G.L. Ryan, X. Feng, F. Fanelli, D.L. Segaloff (2007). Intrinsic differences in the response of the human lutropin receptor versus the human follitropin receptor to activating mutations. J. Biol. Chem. 282: 25527-25539.
  67. D. Dell’Orco, P.G. De Benedetti, F. Fanelli (2007). In silico screening of mutational effects on transmembrane helix dimerization: insights from rigid-body docking and molecular dynamics simulations. J. Phys. Chem. B. 111: 9114-9124.
  68. D. Dell’Orco, P.G. De Benedetti, F. Fanelli (2007). In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach. BMC Struct. Biol. 7: 37.
  69. D. Dell’Orco, M. Seeber, F. Fanelli (2007). Monomeric dark rhodopsin holds the molecular determinants for transducin recognition: insights from computational analysis. FEBS Lett. 581: 944-948.
  70. F. Fanelli (2007). Dimerization of the lutropin receptor: insights from computational modeling. Mol. Cell. Endocrinol. 260-262: 59-64.
  71. D. Puett, Y. Li, G. DeMars, K. Angelova, F. Fanelli (2007). A functional transmembrane complex: the luteinizing hormone receptor with bound ligand and G protein. Mol. Cell. Endocrinol. 260-262: 126-136.
  72. F. Fanelli, P.G. De Benedetti (2006). Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling. J. Comput. Aided Mol. Des. (7-8): 449-461.
  73. M. Seeber, F. Fanelli, E. Paci, A. Caflisch (2006). Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane. Biophys. J. 91: 3276-3284.
  74. D. Casciari, M. Seeber, F. Fanelli (2006). Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinformatics 7: 340.
  75. F. Fanelli, S. Ferrari (2006). Prediction of MEF2A-DNA interface by rigid body docking: A tool for fast estimation of protein mutational effects on DNA binding. J. Struct. Biol. 153: 278-283.
  76. D. Dell’Orco, P. G. De Benedetti, F. Fanelli (2006). Single Amino Acid Contributions to Binding Affinity in Enzyme-Inhibitor Interactions: a Docking-Based Screening of BPTI-Beta Trypsin interaction. In NIC Workshop 2006, From Computational Biophysics to Systems Biology (Jan Meinke, Olav Zimmermann, Sandipan Mohanty, Ulrich H.E. Hansmann Eds.) Vol. 34, 67-72.
  77. S. Cotecchia, F. Fanelli, A. Scheer, T. Costa (2006). Constitutive activity at the alpha1-adrenoceptors: past and future implications. In Methods and Principles in Medicinal Chemistry (R. Mannhold, H. Kubinyi and G. Folkers Eds) Vol. 24 G Protein-Coupled Receptors as Drug Targets. Analysis of Activation and Constitutive Activity (R. Seifert and T. Wieland Editors.), WILEY-VCH Verlag, 159-176.
  78. F. Fanelli, D. Dell’Orco (2005). Rhodopsin activation follows pre-coupling with transducin: inferences from computational analysis. Biochemistry, 44: 14695-14700.
  79. D. Puett, Y. Li, K. Angelova, G. DeMars, T. P. Meehan, F. Fanelli, P. Narayan (2005). Structure-Function Relationships of the Luteinizing Hormone Receptor. Ann N Y Acad Sci., 1061: 41-54.
  80. D. Dell’Orco, M. Seeber, P. G. De Benedetti and F. Fanelli (2005). Probing fragment complementation by rigid-body docking: In silico reconstitution of calbindin D9k. J. Chem. Inf. Model. 45: 1429-1438.
  81. F. Fanelli, P.G. De Benedetti (2005). Computational modeling approaches to Structure-Function Analysis of G Protein-Coupled Receptors. Chem. Rev. 105: 3297-3351.
  82. N. Favre, F. Fanelli, M. Missotten, J. Wilson, M. di Tiani, C. Rommel, A. Scheer (2005). The DRY motif as a molecular switch of the human oxytocin receptor. Biochemistry 44: 9990-10008.
  83. M. Zhang, D. Mizrachi, F. Fanelli, D.L. Segaloff (2005). The formation of a salt bridge between helices 3 and 6 is responsible for the constitutive activity and lack of hormone responsiveness of the naturally occurring L457R mutation of the human lutropin receptor. J. Biol. Chem. 280: 26169-26176.
  84. C. Ambrosio, P. Molinari, F. Fanelli, Y. Chuman, M. Sbraccia, O. Ugur, T. Costa (2005). Different structural requirements for the constitutive and agonist-induced activities of the β2-adrenergic receptor. J. Biol. Chem. 280: 23464-23474.
  85. Leonardi, D. Barlocco, F. Montesano, G. Cignarella, G. Motta, R. Testa, E. Poggesi, M. Seeber, P. G. De Benedetti, F. Fanelli (2004). Synthesis, screening and molecular modeling of new potent and selective antagonists at the α1d-adrenergic receptor. J. Med. Chem. 47: 1900-1918.
  86. F. Fanelli, M. Verhoef-Post, M. Timmerman, A. Zeilemaker, J. W.M. Martens and A. P.N. Themmen (2004). Insight into mutation-induced activation of the lutropin receptor: molecular simulations predict the functional behavior of engineered mutants at M398. Mol. Endocrinol. 18: 1499-1508.
  87. R. M. Vitale, C. Pedone, P.G. De Benedetti and F. Fanelli (2004). Structural features of the inactive and active states of the melanin-concentrating hormone receptors: insights from molecular simulations. PROTEINS 56: 430-448.
  88. S. Cotecchia, L. Stanasila, D. Diviani, K. Björklöf, O. Rossier and F. Fanelli (2004). Structural determinants involved in the activation and regulation of G protein-coupled receptors: lessons from the α1-adrenegic receptor subtypes Biol. Cell 96: 327-333.
  89. S. Ferre, F. Ciruela, M. Canals, D. Marcellino, J. Burgueno, V. Casado, J. Hillion, M.Torvinen, F. Fanelli, P.G. De Benedetti, S. R. Goldberg, M. Bouvier, K. Fuxe, L. F. Agnati, C. Lluis, R. Franco, A. Woods (2004). Adenosine A2A-dopamine D2 receptor–receptor heteromers. Targets for neuro-psychiatric disorders Parkinsonism Related Dis. 10: 265-271.
  90. F. Fanelli (2004) Computational modeling of LH receptor. Proceedings of the 12th International Congress of Endocrinology. 119-123.
  91. M. Seeber, P.G. De Benedetti, F. Fanelli (2003). Molecular dynamics simulations of the ligand-induced chemical information transfer in the 5-HT1A receptor, J. Chem. Inf. Comp. Sci. 43: 1520-1531.
  92. M. Canals, D. Marcellino, F. Fanelli F. Ciruela, P.G. De Benedetti, S. R. Goldberg, K. Fuxe, L. F. Agnati, A. S. Woods, S. Ferré, C. Lluis, M. Bouvier, R. Franco (2003). Adenosine A2A-dopamine D2 receptor-receptor heteromerization. I. Qualitative and quantitative assessment by Fluorescence and Bioluminiscence Energy Transfer. J. Biol. Chem. 278: 46741-46749.
  93. S. Cotecchia, F. Fanelli, T. Costa (2003). Constitutively active G protein-coupled receptor mutants: implications on receptor function and drug action. Assay Drug Dev. Techn. 1: 311-316.
  94. M. Ascoli, F. Fanelli, D.L. Segaloff (2002). The lutropin/choriogonadotropin receptor, a 2002 perspective. Endocr. Rev. 23: 141-174.
  95. P.J. Greasley, F. Fanelli, O. Rossier, L. Abuin, S. Cotecchia (2002). Mutagenesis and modelling of the α1b-adrenergic receptor highlights the role of the helix3/helix6 interface in receptor activation. Mol. Pharmacol. 61: 1-8.
  96. K. Angelova, F. Fanelli, D. Puett (2002). A model for constitutive lutropin receptor activation based on molecular simulation and engineered mutations in transmembrane helices 6 and 7. J. Biol. Chem. 277: 32202-32213.
  97. F. Fanelli,, D. Puett (2002). Structural Aspects of the Luteinizing Hormone Receptor: Information from Molecular Modeling and Mutagenesis. Endocrine 18:285-293.
  98. S. Cotecchia, K. Björklöf, O. Rossier, L. Stanasila, P. Greasley, F. Fanelli (2002). The a1b-adrenergic receoptor subtype: molecular properties and physiological implications. J. Recept. Signal. Transduct. 22: 1-16.
  99. F. Fanelli (2002). Understanding the mutation-induced activation of the lutropin receptor from computer simulation. In Testicular Tangrams (F.F.G. Rommerts and K.J. Teerds Eds), Springer-Verlag Berlin Heidelberg, 29-38.
  100. H. Shinozaki, F. Fanelli, X. Liu, K. Nakamura, D.L. Segaloff (2001). Pleiotropic Effects of Substitutions of a Highly Conserved Leucine in Transmembrane Helix III of the Human Lutropin/Choriogonadotropin Receptor With Respect to Constitutive Activation and Hormone Responsiveness. Mol. Endocrinol. 15: 972-984.
  101. D. Barlocco, G. Cignarella, V. Dal Piaz, M.P. Giovannoni, P.G. De Benedetti, F. Fanelli, F. Montesano, E. Poggesi, A. Leonardi (2001). Phenylpiperazinylalkylamino substituted pyridazinones as potent alpha-1 adrenoceptor antagonists, J. Med. Chem., 44: 2403-2410.
  102. P.J. Greasley, F. Fanelli, A. Scheer, L. Abuin, M. Nenniger-Tosato, P.G. De Benedetti, S. Cotecchia (2001). Mutational and Computational Analysis of the α1b-Adrenergic Receptor. Involvement of Basic and Hydrophobic residues in Receptor Activation and G protein Coupling. J. Biol. Chem. 276: 46485-46494.
  103. F. Fanelli, A. Themmen, D. Puett (2001). Lutropin receptor function: insights from natural, enginered and computer-simulated mutations. IUBMB Life 51:149-155.
  104. P.G. De Benedetti, F. Fanelli, M.C. Menziani, M. Cocchi (2000). The ad hoc supermolecule approach to receptor ligand design. J. Mol. Struct. (THEOCHEM) 503: 1-16.
  105. F. De Rienzo, F. Fanelli, M.C. Menziani, P.G. De Benedetti (2000). Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450IIIA4. J. Comput. Aid. Mol. Des. 14: 93-116.
  106. Scheer, T. Costa, F. Fanelli, S. Mhaouty-Kodja, L. Abuin, M. Nenniger-Tosato, P.G. De Benedetti, S. Cotecchia (2000). Mutational analysis of the highly conserved arginine within the Glu/Asp-Arg-Tyr motif of the α1b-adrenergic receptor: effects on receptor isomerization and activation. Mol. Pharmacol. 57: 219-233.
  107. F. Fanelli (2000). Theoretical study on mutation-induced activation of the luteinizing hormone receptor, J. Mol. Biol. 296: 1337-1355.
  108. S. Cotecchia, O. Rossier, F. Fanelli, A. Leonardi, Pier G. De Benedetti (2000). The α1a and α1b-adrenergic receptor subtypes: molecular mechanisms of receptor activation and of drug action. Pharmaceutica Acta Helvetiae 74: 173-179.
  109. B. Chini, F. Fanelli (2000). Molecular basis of ligand binding and receptor activation in the oxytocin/vasopressin receptor family. Exp. Physiol. 85S: 59-66.
  110. Latronico, H. Shinozaki, G. Guerra Jr., M.A.A. Pereira, S.H.V.L. Marini, M.T.M. Baptista, I. J. P. Arnhold, F. Fanelli, B.B. Mendonca, D.L. Segaloff (2000). Gonadotropin-independent precocious puberty due to luteinizing hormone receptor mutations in brazilian boys: a novel constitutively activating mutation in the first transmembrane helix. J. Clin. Endocr. Metab. 85: 4799-4805.
  111. F. Fanelli, P. Barbier, D. Zanchetta, P.G. De Benedetti, B. Chini (1999). Activation Mechanism of Human Oxytocin Receptor: A Combined Study of Experimental and Computer-Simulated Mutagenesis. Mol. Pharmacol. 56: 214-225.
  112. Scheer, F. Fanelli, D. Diviani, P.G. De Benedetti, S. Cotecchia (1999). Structure-Function Relationships of the α1b-Adrenergic Receptor. Eur. Urol. 36S: 11-16.
  113. F. Fanelli, M. Menziani, A. Scheer, S. Cotecchia, P.G. De Benedetti (1999). Theoretical study on the electrostatically driven step of receptor-G protein recognition. PROTEINS 37: 145-156.
  114. F. Fanelli, M. Menziani, A. Scheer, S. Cotecchia, P.G. De Benedetti (1999). Theoretical study on receptor-G protein recognition: new insights into the mechanism of the a1b-adrenergic receptor activation. Internat. J. of Quantum Chem. 73:71-83.
  115. O. Rossier, L. Abuin, F. Fanelli, A. Leonardi, S. Cotecchia (1999). Inverse Agonism and Neutral Antagonism at α1a- and α1b-Adrenergic Receptor Subtypes. Mol. Pharmacol. 56: 858-866.
  116. S. Cotecchia, F. Fanelli, A. Scheer, P.G. De Benedetti (1999). Constitutively active receptor mutants as probes for studying the mechanisms underlying G protein-coupled receptor activation. in Receptor Biochemistry and Methodology (C. Strader and D. Sibley eds) Vol. III: Structure-Function Analysis of G Protein-Coupled Receptors (J. Wess Editor), Wiley-Liss Pub., New York, 167-183.
  117. F. Montesano, D. Barlocco, V. Dal Piaz, A. Leonardi, E. Poggesi, F. Fanelli, P.G. De Benedetti (1998). Isoxazolo-3,4-d-pyridazin-7-(6H)-ones and their corresponding 4,5-disubstituted-3-(2H) pyridazinone analogues as new substrates for α1-adrenoceptor selective antagonists: synthesis, modeling and binding studies. Bioorg. Med. Chem. 6: 925-935.
  118. F. Fanelli, M.C. Menziani, A. Scheer, S. Cotecchia, P.G. De Benedetti (1998). Ab initio modeling and molecular dynamics simulation of the α1b-adrenergic receptor activation. Methods Companion to Methods in Enzymology 14: 302-317.
  119. M. Montorsi, M. C. Menziani, M. Cocchi, F. Fanelli, P.G. De Benedetti (1998). Computer Modeling of Size and Shape Descriptors of α1-Adrenergic Receptor Antagonists and Quantitative Structure-Affinity/Selectivity Relationships Methods Companion to Methods in Enzymology 14: 239-254.
  120. D.S. Bahia, A. Wise, F. Fanelli, M. Lee, S. Rees, G. Milligan (1998). Hydrophobicity of residue351 of the G protein Gi1α determines the extent of activation by the α2A-adrenoceptor. Biochemistry 37: 11555-11562.
  121. S. Cotecchia, A. Scheer, D. Diviani, F. Fanelli, P.G. De Benedetti (1998). Molecular Mechanisms involved in the activation and regulation of the α1-adrenergic receptor subtypes. Il Farmaco 53: 273-277.
  122. B. Chini, E. Albertazzi, P.G. De Benedetti, F. Fanelli (1998). Identification of a constitutively active mutant of the human oxytocin receptor. Adv. Exp. Med. Biol. 449: 367-369.
  123. C.M. Reaper, F. Fanelli, S.D. Buckingham, N.S. Millar, D.B. Sattelle (1998). Antagonist profile and molecular dynamic simulation of a Drosophila melanogaster muscarinic acetylcholine receptor. Receptor Channel. 5: 331-345.
  124. D. Barlocco, G. Cignarella, F. Fanelli, B. Vitalis, P. Matyus, PG. De Benedetti (1997). Thienocycloheptapyridazines as new muscarinic agents Drug Design and Discovery 14: 273-290.
  125. M. Cocchi, F. Fanelli, M. Menziani, P.G. De Benedetti (1997). Conformational analysis and theoretical quantitative size and shape-affinity relationships of N4-protonated N1-arylpiperazine 5-HT1A serotoninergic ligands. J. Mol. Struct. (THEOCHEM) 397: 129-145.
  126. P.G. De Benedetti, F. Fanelli, M. Menziani, M. Cocchi, R. Testa, A. Leonardi (1997). α1-Adrenoceptor Subtype Selectivity: Molecular Modelling and Theoretical Quantitative Structure-Affinity Relationships. Bioorg. Med. Chem. 5: 809-816.
  127. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti, S. Cotecchia (1997). The activation process of the α1b-adrenergic receptor: potential role of protonation and hydrophobicity of a highly conserved aspartate. Proc. Natl. Acad. Sci. USA 94: 808-813.
  128. M.C. Menziani, F. Fanelli, P.G. De Benedetti (1997). Theoretical Investigation of IL-6 Multiprotein Receptor Assembly. PROTEINS 29: 528-544.
  129. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti, S. Cotecchia (1997). Constitutively active α1B-adrenergic receptor mutants: potential mechanisms underlying receptor activation. Pharmacochemistry Library 28: 421-431.
  130. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti, S. Cotecchia (1996). Constitutively active mutants of the α1b-adrenergic receptor: role of highly conserved polar amino acids in receptor activation. EMBO J. 15: 3566-3578.
  131. M.C. Menziani, F. Fanelli, P.G. De Benedetti (1996). Computational Simulations of Stem-Cell Factor/c-Kit Receptor Interaction. PROTEINS 26: 42-54.
  132. D. Barlocco, F. Fanelli, G. Cignarella, S. Villa, F. Cattabeni, W. Balduini, M. Cimino, P.G. De Benedetti (1996). 2-(Substituted)amino-2,8-diazaspiro[4,5]decan-1,3-diones as potential muscarinic agonists: synthesis, modeling and binding studies. Drug Design and Discovery 14: 129-143.
  133. S. Cotecchia, A. Scheer, F. Fanelli, T. Costa (1996). Molecular mechanisms underlying the activation and regulation of the α1b-adrenergic receptor. Biochem. Soc. Transact. 24: 959-963.
  134. A. Cavalli, F. Fanelli, C. Taddei, P.G. De Benedetti, S. Cotecchia (1996). Amino acids of the α1B-adrenergic receptor involved in agonist binding: further differences in docking catecholamines to receptor subtypes. FEBS Lett. 399: 9-13.
  135. M. C. Menziani, F. Fanelli, M. Cocchi, P. G. De Benedetti (1996). The Heuristic-Direct approach to Quantitative Structure-Activity Relationship Analysis of Ligand-G Protein Coupled Receptor Complexes. In Membrane Protein Models: Experiment, Theory and Speculation (J. Findley, Ed.) Bios Science Pub., 113-131.
  136. M. Cocchi, M.C. Menziani, F. Fanelli, P.G. De Benedetti (1995). Theoretical quantitative structure-activity relationship analysis of congeneric and non congeneric α1-adrenoceptor antagonists: a chemometric study. J. Mol. Struct. (THEOCHEM) 331: 79-93.
  137. F. Fanelli, M.C. Menziani, M. Cocchi, P.G. De Benedetti (1995). Comparative molecular dynamics study of the seven-helix bundle arrangement of G-protein coupled receptors. J. Mol. Struct. (THEOCHEM) 333: 49-69.
  138. M.C. Menziani, M. Cocchi, F. Fanelli, P.G. De Benedetti (1995). Quantitative structure-affinity/selectivity relationship analysis on three-dimensional models of the complexes between the ETA and ETB receptors and C-terminal endothelin hexapeptide antagonists. J. Mol. Struct. (THEOCHEM) 333: 243-248.
  139. P.G. De Benedetti, M.C. Menziani, M. Cocchi, F. Fanelli (1995). Prototropic molecular forms and theoretical descriptors in QSAR analysis. J. Mol. Struct. (THEOCHEM) 333:1-17.
  140. F. Fanelli, M.C. Menziani, P.G. De Benedetti (1995). Computer simulations of signal transduction mechanism in α1b-adrenergic and m3-muscarinic receptors. Protein Engineering, Design and Selection 8: 557-564.
  141. F. Fanelli, M.C. Menziani, P.G. De Benedetti (1995). Molecular Dynamics Simulations of m3-Muscarinic Receptor Activation and QSAR Analysis. Bioorg. Med. Chem. 3: 1465-1477.
  142. P.G. De Benedetti, M.C. Menziani, F. Fanelli, M. Cocchi (1995). The Heuristic-Direct Approach to QSAR Analysis of Ligand-G-Protein Coupled Receptor Complexes. In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications (F. Sanz, J. Giraldo and F. Manaut Eds.) Prous Science Pub. 526-527.
  143. M.C. Menziani, M. Cocchi, F. Fanelli, P.G. De Benedetti (1995). Theoretical QSAR analysis on three dimensional models of the complexes between peptide and non-peptide antagonists with the ETA and ETB receptors. In QSAR and Molecular Modelling: Concepts, Computational Tools and Biological Applications. (F. Sanz, J. Giraldo and F. Manaut Eds.) Prous Science Pub., 519-525.
  144. F. Fanelli, M.C. Menziani, A. Carotti, P.G. De Benedetti (1994). Theoretical Quantitative Structure-Activity Relationship Analysis on Three Dimensional Models of Ligand-m1 Muscarinic Receptor Complexes. Bioorg. Med. Chem. 2: 195-211.
  145. P.G. De Benedetti, M. Cocchi, M.C. Menziani, F. Fanelli (1994). Theoretical quantitative size and shape activity and selectivity analyses of 5-HT1A serotonin and α-adrenergic receptor ligands. J. Mol. Struct. (THEOCHEM) 305: 101-110.
  146. F. Fanelli, M.C. Menziani, M. Cocchi, A. Leonardi, P.G. De Benedetti (1994). The heuristic-direct approach to theoretical quantitative structure activity relationship analysis of α1- adrenoceptor ligands. J. Mol. Struct. (THEOCHEM) 314: 265-276.
  147. F. Fanelli, M.C. Menziani, A. Carotti, P.G. De Benedetti (1993). Theoretical quantitative structure-activity analysis of quinuclidine-based muscarinic cholinergic receptor ligands. J. Mol. Struct. (THEOCHEM) 283: 63-71.
  148. C. Altomare, A. Carotti, S. Cellamare, F. Fanelli, F. Gasparrini, C. Villani, P.-A. Carrupt, B. Testa (1993). Enantiomeric resolution of sulfoxides on a DACH-DNB chiral stationary phase: a quantitative structure-enantioselective retention relationship (QSERR) study. Chirality 5: 527-537.
  149. P.G. De Benedetti, M. Cocchi, M.C. Menziani, F. Fanelli (1993). Theoretical quantitative structure-activity analysis and pharmacophore modelling of selective non congeneric α1a-adrenergic antagonists. J. Mol. Struct. (THEOCHEM) 280: 283-290.
  150. P.G. De Benedetti, M.C. Menziani, F. Fanelli and M. Cocchi (1993). The heuristic-direct approach to quantitative structure-activity relationship analysis. J. Mol. Struct. (THEOCHEM) 285: 147-153.
  151. F. Fanelli, M.C. Menziani, M. Cocchi, P.G. De Benedetti (1993). Three dimensional molecular modeling of the α1a-adrenoceptor. Direct 3D-QSAR modeling of selective antagonists. In Trends in QSAR and Molecular Modelling 92. (C.G. Wermuth Ed.), Escom, Leiden, 260-263.
  152. P. Venturelli, M.C. Menziani, M. Cocchi, F. Fanelli, P.G. De Benedetti (1992). Molecular modeling and quantitaive structure-activity relationship analysis using theoretical descriptors of 1,4-benzodioxan (WB-4101) related compounds α1-adrenergic antagonists. J. Mol. Struct. (THEOCHEM) 276: 327-340.
  153. G. Rastelli, F. Fanelli, M.C. Menziani, M. Cocchi, P.G. De Benedetti (1991). Conformational analysis, molecular modeling and quantitative structure-activity relationships studies of 2,4-diamino-6,7-dimethoxy-2-substituted quinazoline α1-adrenergic antagonists. J. Mol. Struct. (THEOCHEM) 251: 307-318.