Publications

  1. S. 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.
  2. S. Mariani, D. Dell’Orco, A. Felline, F. Raimondi and F. Fanelli (2013) Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases. PLoS Comput Biol 9: e1003207.
  3. 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., 9:2504-2508.
  4. 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.
  5. F. Fanelli, F. Raimondi (2013). Nucleotide binding affects intrinsic dynamics and structural communication in Ras GTPases. Curr. Pharm. Des., 19:4214-4225.
  6. F. Raimondi, A. Felline, G. Portella, M. Orozco, and F. Fanelli (2013). Light on the structural communication in Ras GTPases. J. Biomol. Struct. Dyn., 31:142-157.
  7. M. Giannotta, C. Ruggiero, M. Grossi, J. Cancino, M. Capitani, T. Pulvirenti, G. M. Consoli, C. Geraci, F. Fanelli, A. Luini, and 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.
  8. F. Fanelli and 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.
  9. G. DeMars, F. Fanelli and D. Puett (2011). The extreme C-terminal region of Galphas differentially couples to the luteinizing hormone and beta2-adrenergic receptors. Mol. Endocrinol. 25:1416-30.
  10. F. Fanelli, M. Mauri, V. Capra, F. Raimondi, F. Guzzi, M. Ambrosio, G. E. Rovati and M. Parenti (2011). Light on the structure of thromboxane A2 receptor hetero-dimers Cell. Mol. Life Sci. 68:3109-20.
  11. F. Raimondi, G. Portella, M. Orozco and F. Fanelli (2011). Nucleotide binding switches the information flow in ras GTPases. PLoS Comput. Biol. 7:e1001098.
  12. F. Fanelli and A. Felline (2011). Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor. Biochim. Biophys. Acta 1808:1256-1266.
  13. K. Angelova, A. Felline, M. Lee, M. Patel, D. Puett and 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.
  14. 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.
  15. P. G. De Benedetti and F. Fanelli (2010). Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR. Drug Discov Today 15:859-866.
  16. D. Puett, K. Angelova, M. R. da Costa, S. W. Warrenfeltz and 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.
  17. A. Carrieri, A. Piergentili, F. Del Bello, M. Giannella, M. Pigini, A. Leonardi, F. Fanelli and 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.
  18. M. Ambrosio, F. Fanelli, S. Brocchetti, F. Raimondi, M. Mauri, G. E. Rovati and 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.
  19. F. Fanelli and M. Seeber (2010). Structural insights into retinitis pigmentosa from unfolding simulations of rhodopsin mutants. FASEB J. 24:3196-3209.
  20. F. Raimondi, M. Orozco and F. Fanelli (2010). Deciphering the deformation modes associated with function retention and specialization in members of the Ras Superfamily. Structure 18:402-414.
  21. A. 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. 52:5590-602.
  22. A. Felline, M. Seeber, F. Rao and F. Fanelli (2009). Computational screening of rhodopsin mutations associated with Retinitis Pigmentosa. J. Chem. Theory Comput. 5:2472-2485.
  23. D. Dell’Orco, H. Schmidt, S. Mariani and F. Fanelli (2009). Network level analysis of light adaptation in rod cells under normal and altered conditions. Mol. Biosystems 5:1232-1246.
  24. P.G. De Benedetti and F. Fanelli (2009). Ligand-target communication and drug design. Curr. Protein Pept. Sci. 10:186-193.
  25. F. Fanelli, P.G. De Benedetti, F. Raimondi and M. Seeber (2009). Intra and intermolecular communication in GPCRs. Curr. Prot. Pept. Sci. 10:173-185.
  26. 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, and C. Sotriffer (2008). Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J. Med. Chem. 51:6237-6255.
  27. Casciari, C., D. Dell’Orco, and 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.
  28. Dell’Orco, D., C. Casciari, and F. Fanelli (2008). Quaternary structure predictions and estimation of mutational effects on the free energy of dimerization of a -barrel transmembrane protein. J. Struct. Biol. 163:155-162.
  29. F. Fanelli and D. Dell’Orco (2008). Dark and photoactivated rhodopsin share common binding modes to transducin. FEBS Lett. 582:991-996.
  30. F. Raimondi, M. Seeber, P.G. De Benedetti, and F. Fanelli (2008). Mechanisms of inter- and intra-molecular communication in GPCRs and G proteins. J. Am. Chem. Soc. 130:4310-4325.
  31. X. Feng, T. Muller, D. Mizrachi, F. Fanelli, and 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.
  32. K. Angelova, F. Fanelli, and D. Puett (2008). Contributions of intracellular loops 2 and 3 of the lutropin receptor in gs coupling. Mol. Endocrinol. 22:126-38.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. F. Fanelli (2007). Dimerization of the lutropin receptor: insights from computational modeling. Mol. Cell. Endocrinol. 260-262:59-64.
  38. D. Puett, Y. Li, G. DeMars, K. Angelova, and F. Fanelli (2007). A functional transmembrane complex: the luteinizing hormone receptor with bound ligand and G protein. Mol. Cell. Endocrinol. 260-262:126-136.
  39. F. Fanelli and 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.
  40. 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.
  41. D. Casciari, M. Seeber and F. Fanelli (2006). Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinformatics 7:340.
  42. F. Fanelli and S. Ferrari (2006). High performance prediction of MEF2A-DNA interface by rigid body docking: an effective tool for in silico estimation of protein mutational effects on DNA binding. J. Struct. Biol. 153:278-283.
  43. F. Fanelli and D. Dell’Orco (2005). Rhodopsin activation follows pre-coupling with transducin: inferences from computational analysis. Biochemistry, 44:14695-14700.
  44. D. Puett, Y. Li, K. Angelova, G. DeMars, T. P. Meehan, F. Fanelli, and P. Narayan (2005). Structure-Function Relationships of the Luteinizing Hormone Receptor. Ann N Y Acad Sci., 1061:41-54.
  45. 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. and Mod. 45:1429-1438.
  46. F. Fanelli and P.G. De Benedetti (2005).Computational modeling approaches to Structure-Function Analysis of G Protein-Coupled Receptors. Chem. Rev. 105: 3297-3351.
  47. N. Favre, F. Fanelli, M. Missotten, J. Wilson, M. di Tiani, C. Rommel and A. Scheer (2005). The DRY motif as a molecular switch of the human oxytocin receptor. Biochemistry 44: 9990-10008.
  48. M. Zhang, D. Mizrachi, F. Fanelli and 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.
  49. C. Ambrosio, P. Molinari, F. Fanelli, Y. Chuman, M. Sbraccia, O. Ugur, and T. Costa (2005). Different structural requirements for the constitutive and agonist-induced activities of the 2-adrenergic receptor. J. Biol. Chem., 280:23464-23474.
  50. A. Leonardi, D. Barlocco, F. Montesano, G. Cignarella, G. Motta, R. Testa, E. Poggesi, M. Seeber, P. G. De Benedetti and 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.
  51. 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.
  52. 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.
  53. 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.
  54. 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 and A. Woods (2004). Adenosine A2A-dopamine D2 receptor–receptor heteromers. Targets for neuro-psychiatric disorders Parkinsonism Related Dis. 10:265–271.
  55. M. Seeber, Pier G. De Benedetti and 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.
  56. M. Canals, D. Marcellino, F. Fanelli F. Ciruela, P. de Benedetti, S. R. Goldberg, K. Fuxe, L. F. Agnati, A. S. Woods, S. Ferré, C. Lluis, M. Bouvier, and 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.
  57. S. Cotecchia, F. Fanelli and T. Costa (2003). Constitutively active G protein-coupled receptor mutants: implications on receptor function and drug action. Assay Drug Dev. Techn. 1: 311-316.
  58. M. Ascoli, F. Fanelli and D. L. Segaloff (2002). The lutropin/choriogonadotropin receptor, a 2002 perspective. Endocr. Rev. 23:141-174.
  59. P.J. Greasley, F. Fanelli, O. Rossier, L. Abuin and 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.
  60. K. Angelova, F. Fanelli, and D. Puett (2002). Engineered and Simulated Mutations in Transmembrane Helices 6 and 7 of the Lutropin Receptor: A Model for Constitutive and Ligand-mediated Receptor Activation. J. Biol. Chem. 277: 32202-32213.
  61. F. Fanelli and D. Puett (2002). Structural Aspects of the Luteinizing Hormone Receptor: Information from Molecular Modeling and Mutagenesis. Endocrine, 18:285-293.
  62. S. Cotecchia, K. Björklöf, O. Rossier, L. Stanasila, P. Greasley and F. Fanelli (2002). The α1b-adrenergic receoptor subtype: molecular properties and physiological implications. J. Recept. Sig. Transd. 22:1-16.
  63. H. Shinozaki, F. Fanelli, X. Liu, K. Nakamura and 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.
  64. D. Barlocco, G. Cignarella, V. Dal Piaz, M. P. Giovannoni, P. G. De Benedetti, F. Fanelli, F. Montesano, E. Poggesi and A. Leonardi (2001). Phenylpiperazinylalkylamino substituted pyridazinones as potent alpha-1 adrenoceptor antagonists, J. Med. Chem., 44:2403-2410.
  65. P. J. Greasley, F. Fanelli, A. Scheer, L. Abuin, M. Nenniger-Tosato, P.G. De Benedetti and 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.
  66. F. Fanelli, A. Themmen and D. Puett (2001). Lutropin receptor function: insights from natural, enginered and computer-simulated mutations. IUBMB Life 51:149-155.
  67. P.G. De Benedetti, F. Fanelli, M.C. Menziani and M. Cocchi (2000). The ad hoc supermolecule approach to receptor ligand design. J. Mol. Struct. (THEOCHEM) 503:1-16.
  68. F. De Rienzo, F. Fanelli, M.C. Menziani and 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.
  69. A. Scheer, T. Costa, F. Fanelli, S. Mhaouty-Kodja, L. Abuin, M. Nenniger-Tosato, P.G. De Benedetti and 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.
  70. F. Fanelli (2000). Theoretical study on mutation-induced activation of the luteinizing hormone receptor, J. Mol. Biol. 296:1337-1355.
  71. S. Cotecchia, O. Rossier, F. Fanelli, A. Leonardi and 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.
  72. B. Chini and F. Fanelli (2000). Molecular basis of ligand binding and receptor activation in the oxytocin/vasopressin receptor family. Exp. Physiol. 85S:59-66.
  73. A. C. 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 and 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.
  74. F. Fanelli, P. Barbier, D. Zanchetta, P.G. De Benedetti and B. Chini (1999). Activation Mechanism of Human Oxytocin Receptor: A Combined Study of Experimental and Computer-Simulated Mutagenesis. Mol. Pharmacol. 56:214-225.
  75. F. Fanelli, M.C. Menziani, A. Scheer, S. Cotecchia and P.G. De Benedetti (1999). Theoretical study on receptor-G protein recognition: new insights into the mechanism of the α1b-adrenergic receptor activation. International Journal of Quantum Chemistry 73:71-83.
  76. A. Scheer, F. Fanelli, D. Diviani, P.G. De Benedetti and S. Cotecchia (1999). Structure-Function Relationships of the α1b-Adrenergic Receptor. Eur. Urol. 36S:11-16.
  77. F. Fanelli, M. Menziani, A. Scheer, S. Cotecchia and P.G. De Benedetti (1999). Theoretical study on the electrostatically driven step of receptor-G protein recognition. PROTEINS 37:145-156.
  78. O. Rossier, L. Abuin, F. Fanelli, A. Leonardi and S. Cotecchia (1999). Inverse Agonism and Neutral Antagonism at α1a- and α1b-Adrenergic Receptor Subtypes. Mol. Pharmacol. 56:858-866.
  79. F. Montesano, D. Barlocco, V. Dal Piaz, A. Leonardi, E. Poggesi, F. Fanelli and 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.
  80. F. Fanelli, M.C. Menziani, A. Scheer, S. Cotecchia and 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.
  81. M. Montorsi, M. C. Menziani, M. Cocchi, F. Fanelli and 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.
  82. D.S. Bahia, A. Wise, F. Fanelli, M. Lee, S. Rees and G. Milligan (1998). Hydrophobicity of residue351 of the G protein Gi1α determines the extent of activation by the α2A-adrenoceptor. Biochemistry 37:11555-11562.
  83. S. Cotecchia, A. Scheer, D. Diviani, F. Fanelli and P.G. De Benedetti (1998). Molecular Mechanisms involved in the activation and regulation of the α1-adrenergic receptor subtypes. Il Farmaco 53:273-277.
  84. B. Chini, E. Albertazzi, P.G. De Benedetti and F. Fanelli (1998). Identification of a constitutively active mutant of the human oxytocin receptor. Adv. Exp. Med. Biol. 449:367-369.
  85. C.M. Reaper, F. Fanelli, S.D. Buckingham, N.S. Millar and D.B. Sattelle (1997). Antagonist profile and molecular dynamic simulation of a Drosophila melanogaster muscarinic acetylcholine receptor. Receptor. Channel. 5:331-345.
  86. D. Barlocco, G. Cignarella, F. Fanelli, B. Vitalis, P. Matyus and PG. De Benedetti (1997). Thienocycloheptapyridazines as new muscarinic agents Drug Design and Discovery 14:273-290.
  87. M. Cocchi, F. Fanelli, M. Menziani and 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.
  88. P.G. De Benedetti, F. Fanelli, M. Menziani, M. Cocchi, R. Testa and A. Leonardi (1997). α1-Adrenoceptor Subtype Selectivity: Molecular Modelling and Theoretical Quantitative Structure-Affinity Relationships. Bioorg. Med. Chem. 5:809-816.
  89. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti and 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.
  90. M.C. Menziani, F. Fanelli and P.G. De Benedetti (1997). Theoretical Investigation of IL-6 Multiprotein Receptor Assembly. PROTEINS 29:528-544.
  91. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti and 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.
  92. M.C. Menziani, F. Fanelli and P.G. De Benedetti (1996). Computational Simulations of Stem-Cell Factor/c-Kit Receptor Interaction. PROTEINS 26:42-54.
  93. D. Barlocco, F. Fanelli, G. Cignarella, S. Villa, F. Cattabeni, W. Balduini, M. Cimino and 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.
  94. S. Cotecchia, A. Scheer, F. Fanelli and T. Costa (1996). Molecular mechanisms underlying the activation and regulation of the α1b-adrenergic receptor. Biochem. Soc. T. 24:959-963.
  95. A. Cavalli, F. Fanelli, C. Taddei, P.G. De Benedetti and 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.
  96. M. Cocchi, M.C. Menziani, F. Fanelli and 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.
  97. F. Fanelli, M.C. Menziani, M. Cocchi and 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.
  98. M.C. Menziani, M. Cocchi, F. Fanelli and 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.
  99. P.G. De Benedetti, M.C. Menziani, M. Cocchi and F. Fanelli (1995). Prototropic molecular forms and theoretical descriptors in QSAR analysis. J. Mol. Struct. (THEOCHEM) 333:1-17, 1995.
  100. F. Fanelli, C. Menziani and P.G. De Benedetti (1995). Computer simulations of signal transduction mechanism in α1b-adrenergic and m3-muscarinic receptors. Prot. Eng. 8:557-564.
  101. F. Fanelli, M. C. Menziani and P.G. De Benedetti (1995). Molecular Dynamics Simulations of m3-Muscarinic Receptor Activation and QSAR Analysis. Bioorg. Med. Chem. 3:1465-1477.
  102. F. Fanelli, M.C. Menziani, A. Carotti and 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, 1994.
  103. P.G. De Benedetti, M. Cocchi, M. C. Menziani and 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.
  104. F. Fanelli, M.C. Menziani, M. Cocchi, A. Leonardi and 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.
  105. F. Fanelli, M.C. Menziani, A. Carotti and P.G. De Benedetti (1993). Theoretical quantitative structure-activity analysis of quinuclidine-based muscarinic cholinergic receptor ligands. J. Mol. Struct. (THEOCHEM) 283:63-71.
  106. C. Altomare, A. Carotti, S. Cellamare, F. Fanelli, F. Gasparrini, C. Villani, P.-A. Carrupt and 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.
  107. P.G. De Benedetti, M. Cocchi, M.C. Menziani and 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.
  108. 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.
  109. P. Venturelli, M.C. Menziani, M. Cocchi, F. Fanelli and 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.
  110. G. Rastelli, F. Fanelli, M.C. Menziani, M. Cocchi and 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.

Book Chapters

  1. F. Fanelli, A. Felline and F Raimondi (2013). Network analysis to uncover the structural communication in GPCRs. In Receptor-Receptor Interactions (Michael Conn Ed.) book series: Methods Cell. Biol. (L. Wilson, P. Matsudaira, P. Tran Eds.), Academic Press, Elsevier, Amsterdam, The Netherlands, 117: 43-61.
  2. F. Fanelli, M. Seeber, A. Felline, D. Casciari, F. Raimondi (2013). Quaternary structure predictions and structural communication features of GPCR dimers. In Oligomerization in health and disease (J. Giraldo, Ed.), book series: Progress In Molecular Biology And Translational Science (P.M. Conn, Ed.) Academic Press, Elsevier, Amsterdam: The Netherlands, 117:105-142.
  3. F. Fanelli (2013). Modeling the structural communication in supramolecular complexes involving GPCRs. In Membrane Protein Structure and Dynamics Methods and Protocols N. Vaidehi and J. Klein-Seetharaman Eds). Book series: Meth. Mol. Biol.(J. M. Walker Ed), Humana Press, Springer, New York, 914:319-336.
  4. F. Fanelli and 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.
  5. 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.
  6. S. Cotecchia, F. Fanelli, A. Scheer and T. Costa (2005). 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.
  7. 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.
  8. S. Cotecchia, O. Rossier, F. Fanelli, A. Leonardi, P. G. De Benedetti (2000). The a1a and a1b-adrenergic receptor subtypes: molecular mechanisms of receptor activation and of drug action. In: Receptor Chemistry towards the Third Millennium, Proceedings of the 12th Camerino-Noordwijkerhout Symposium. (U. Gulini, M. Gianella, W. Quaglia, G. Marucci. Eds) vol. 31, p. 173-179, Amsterdam:Elsevier.
  9. S. Cotecchia, F. Fanelli, A. Scheer and 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 GPCRs (J. Wess Editor), Wiley-Liss Pub., New York, 167-183.
  10. A. Scheer, F. Fanelli, T. Costa, P.G. De Benedetti and S. Cotecchia (1997). Constitutively active α1B-adrenergic receptor mutants: potential mechanisms underlying receptor activation. in Proceedings of the XIVth International Symposium on Medicinal Chemistry (F. Awooters, Editor), 421-431.
  11. M. C. Menziani, F. Fanelli, M. Cocchi and 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.
  12. P.G. De Benedetti, M.C. Menziani, F. Fanelli and 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.
  13. M. C. Menziani, M. Cocchi, F. Fanelli and 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.
  14. F. Fanelli, M.C. Menziani, M. Cocchi and 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.