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Publications

1.     Genna V., P. Vidossich, E. Ippoliti, P. Carloni, M. DeVivo, A self‐activated mechanism for nucleic acid polymerization catalyzed by DNA/RNA polymerases. Journal of American Chemical Society 2016. In press
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2.     Park K-D, E. A. Muller, V. Kravtsov, P. M. Sass, J. Dreyer, J. M. Atkin, M. B. Raschke, Variable-Temperature Tip-Enhanced Raman Spectroscopy of Single-Molecule Fluctuations and Dynamics, Nano Letters 2016. 16: pp. 479-487.
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3.     Nguyen T. T., D. P. Tran, P. D. Q.  Huy, Z. Hoang, P. Carloni, P.V. Pham, C. Nguyen, M. S. Li, Ligand binding to anti-cancer target CD44 investigated by molecular simulations, Journal of Molecular Modeling 2016. 22(7): n. 165.
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4.     Cong X., C. Cremer, T. Nachreiner, S. Barth, P. Carloni Engineered human angiogenin mutations in the placental ribonuclease inhibitor complex for anticancer therapy: insights from enhanced sampling simulations. Protein Science 2016. 25(8): p. 1451-1460.
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5.     Ghaemi Z., D. Alberga, P. Carloni, A. Laio, G. Lattanzi, Permeability coefficients of lipophilic compounds estimated by computer simulations. Journal of Chemical Theory and Computation 2016. 12 (8): p 4093–4099.
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6.     Pavlin M., G. Rossetti, M. De Vivo, P. Carloni, Carnosine and Homocarnosine Degradation Mechanisms by the Human Carnosinase Enzyme CN1: Insights from Multiscale Simulations. Biochemistry 2016. 55(19): p. 2772-2784.
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7.     Genna V., R. Gaspari, M. Dal Peraro, M. De Vivo, Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η. Nucleic Acids Research 2016. 44(6): p. 2827–2836.
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8.     De Vivo M., M. Masetti, G. Bottegoni, A. Cavalli, The Role of Molecular Dynamics and Related Methods in Drug Discovery, Journal of Medicinal Chemistry 2016. 59 (9): p 4035–4061.
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9.     Kolář M. H., P. Hobza, Computer Modeling of Halogen Bonds and Other σ-Hole Interactions, Chemical Review 2016. 116 (9): p 5155–5187.
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10.  Rossetti G., F. Musiani, E. Abad, D. Dibenedetto, H. Mouhib, C. O. Fernandez and P. Carloni, Conformational ensemble of human a-synuclein physiological form predicted by molecular simulations, Phys. Chem. Chem. Phys. 2016. 18: p. 5702-5706.
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11.  Li J., C. Santambrogio, S. Brocca, G. Rossetti, P. Carloni, R. Grandori, Conformational effects in protein electrospray-ionization mass spectrometry, Mass Spectrometry Reviews 2016. 35(1): p. 111-122.
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12.  Chatain N., R. C. Perera, G. Rossetti, J. Rosso, P. Carloni, M. Schemionek, T. Haferlach, T.H. Brummendorf, S. Scnittger, S. Koschmieder, Rare FLT3 deletion mutants may provide additional treatment options to patients with AML: an approach to individualized medicine, Leukemia 2015. 29(12): p. 2434-2438.
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13.  Calandrini V., G. Rossetti, F. Arnesano, G. Natile, P. Carloni, Computational metallomics of the anticancer drug cisplatin, Journal of Inorganic Biochemistry 2015. 153: p. 231-238.
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14.  Li J., F. Fick, P. verheugd, P. Carloni, B. Lüscher, G. Rossetti, Insight into the Mechanism of Intramolecular Inhibition of the Catalytic Activity of Sirtuin 2 (SIRT2), PLoS ONE 2015. 10(9): p. e0139095.
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15.  Cong X., P. Campomanes, A. Kless, I. Schapitz, M. Wagener, T. Koch, P. Carloni, Structural Determinants for the Binding of Morphinan Agonists to the mu-Opioid Receptor, PLoS ONE 2015. 10(9): p. e0135998.
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16.  Palermo G., A. D. Favia, M. Convertino, M. De Vivo, The molecular basis for dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) inhibition, ChemMedChem (Communication). 2015. 11(12): p. 1252-1258.
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17.  Bolognesi M. L., S. Bongarzone, S. Aulic, H. N. Ai Tran, F. Prati, P. Carloni, G. Legname, Rational approach to an antiprion compound with a multiple mechnism of action, Future Medicinal Chemistry 2015. 7(16): p. 2113-2120.
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18.  Rossetti, G., P D. Dans, I. Gomez-Pinto, I. Ivani, C. González, M. Orozco, M., The structural impact of DNA mismatches, Nucleic Acids Research 2015. 43(8): p. 4309–4321.
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19.  Bochicchio A., G. Rossetti, O. Tabarrini, S. Krauß, P. Carloni, Molecular View of Ligands Specificity for CAG Repeats in Anti-Huntington Therapy, Journal of Chemical Theory and Computation 2015. 11(10): p. 4911-4922.
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20.  Sedlak R., M. H. Kolář, P. Hobza, Polar Flattening and the Strength of Halogen Bonding, Journal of Chemical Theory and Computation 2015. 11(10): p. 4727-4732.
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21.  Finnerty J. J., A. Peyser, P. Carloni, Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation, PLoS ONE 2015. 10(10): p. e0138679.
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22.  Cao R., G. Rossetti, A. Bauer, P. Carloni, Binding of the Antagonist Caffeine to the Human Adenosine Receptor hA2AR in Nearly Physiological Conditions, PLoS ONE 2015. 10(5): p. e0126833.
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23.  Cremer C., H. Braun, R. Mladenov, L. Schenke, X. Cong, E. Jost, T.  H. Brümmendorf, R. Fischer, P. Carloni, S. Barth, Thomas Nachreiner, Novel angiogenin mutants with increased cytotoxicity enhance the depletion of pro-inflammatory macrophages and leukemia cells ex vivo, Cancer Immunology, Immunotherapy 2015. 64(12): p. 1575-1586.
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24.  Sandal M., M. Behrens, A. Brockhoff, F. Musiani, A. Giorgetti, P., W. Meyerhof, Evidence for a Transient Additional Ligand Binding Site in the TAS2R46 Bitter Taste Receptor,  Journal of Chemical Theory and Computation 2015. 11(9): p. 4439-4449.
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25.  Giménez-Dejoz J., M. H. Kolář, F. X. Ruiz, I. Crespo, A. Cousido-Siah, A. Podjarny, O. A. Barski, J. Fanfrlík, X. Parés, J. Farrés, S. Porté, Substrate Specificity, Inhibitor Selectivity and Structure-Function Relationships of Aldo-Keto Reductase 1B15: A Novel Human Retinaldehyde Reductase, PLoS ONE 2015. 10(7): e0134506.
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26.  Palermo G., E. Minniti, M. L. Greco, L. Riccardi, E. Simoni, M. Convertino, C. Marchetti, M. Rosini, C. Sissi, A. Manarini, M. De Vivo, An optimized polyamine moiety boosts potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512, Chemical Communications 2015. 51: p. 14310-14313.
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27.  Fanfrlík J., F. X. Ruiz, A. Kadlčíková, J. Řezáč, A. Cousido-Siah, A. Mitschler, S. Haldar, M. Lepšík, M. H. Kolář, P. Majer, A. D. Podjarny, P. Hobza, The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition, ACS Chemical Biology 2015. 10(7): p. 1637-1642.
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28.  Cremer C., G. Hehmann-Titt, S. Schiffer, G. Melmer, P. Carloni, S. Barth, T. Nachreiner, Engineered Versions of Granzyme B and Angiogenin Overcome Intrinsic Resistance to Apoptosis Mediated by Human Cytolytic Fusion Proteins. In Resistance to Immunotoxins in Cancer Therapy, Springer-Verlag Berlin Heidelberg, 185-220 (2015).
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29.  Rossetti G., D. Dibenedetto, V. Calandrini, A. Giorgetti, P. Carloni, Structural predictions of neurobiologically relevant G-protein coupled receptors and intrinsically disordered proteins, Archives of Biochemistry and Biophysics 2015.  582: p. 91-100.
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30.  Miotto M. C., A. A. Valiente-Gabioud, G. Rossetti, M. Zweckstetter, P. Carloni, P. Selenko, C. Griesinger, A. Binolfi, C. O. Fernandez, Copper Binding to the N-Terminally Acetylated, Naturally Occurring Form of Alpha-Synuclein Induces Local Helical Folding, Journal of the American Chemical Society 2015. 137(20): p. 6444-6447.
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31.  Kolář M. H., P. Deepa, H. Ajani, A. Pecina, P. Hobza, Characteristics of a σ-Hole and the Nature of a Halogen Bond. Topics in Current Chemistry 2015. 359: p. 1-25.
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32.  D'Urzo A., A. Konijnenberg, G. Rossetti, J. Habchi, J. Li, P. Carloni, F. Sobott, S. Longhi, R. Grandori, Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling, Journal of American Society for Mass Spectrometry 2015. 26(3): p. 472-481.
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33.  Arcella A., J. Dreyer, E. Ippoliti, I. Ivani, G. Portella, V. Gabelica, P. Carloni, M. Orozco, Structure and Dynamics of Oligonucleotides in the Gas Phase, Angewandte Chemie 2015. 127(2): p. 477–481.
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34.  Musiani F., G. Rossetti, L. Capece, T. M. Gerger, C. Micheletti, G. Varani, P. Carloni, Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 Transactivation Responsive RNA, Journal of American Chemical Society 2014. 136: p. 15631–15637.
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35.  Calandrini V., J. Dreyer, E. Ippoliti, P. Carloni, Hydration of chloride anions in the NanC Porin from Escherichia coli: a comparative study by QM/MM and MD simulations, Journal of Chemical Physics 2014. 141: p. 22D521.
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36.  D’Amelio N., G. Papamokos, J. Dreyer, P. Carloni, L. Navarini, NMR Studies of Hetero-Association of Caffeine with di-O-Caffeoylquinic Acid Isomers in Aqueous Solution, Food Biophysics 2014. 10(3): p. 235-243.
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37.  Grison A., S. Zucchelli, A. Urzi, I. Zamparo, D. Lazarevic, G. Pascarella, P. Roncaglia, A. Giorgetti, P. Garcia-Esparcia, C. Vlachouli, R. Simone, F. Persichetti, A.R.R. Forrest, Y. Hayashizaki, P. Carloni, I. Ferrer, C. Lodovichi, C. Plessy, the FANTOM Consortium, P. Carninci, S. Gustincich, Mesencephalic dopaminergic neurons express a repertoire of olfactory receptors and respond to odorant-like molecules, BMC Genomics 2014. 15: p. 729.
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38.  Li J., G. Rossetti, J. Dreyer, S. Raugei, E. Ippoliti, B. Lüscher, P. Carloni, Molecular simulation-based structural prediction of protein complexes in mass spectrometry: The human insulin dimer, PLOS Computational Biology 2014. 10(9): p. e1003838.
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39.  Stanyon H. F., X. Cong, Y. Chen, N. Shahidullah, G. Rossetti, J. Dreyer, G. Papamokos, P. Carloni and J. H. Viles, Developing predictive rules for coordination geometry from visible circular dichroism of Copper(II) and Nickel(II) ions in histidine and amide main-chain complexes, FEBS Journals 2014. 281(17): p. 3945-54.
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40.  Kolář M. H., P. Carloni, P. Hobza, Statistical analysis of σ-holes: a novel complementary view on halogen bonding, Physical Chemistry Chemical Physics 2014. 16: p. 19111-19114.
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41.  Calandrini V., T.H. Nguyen, F. Arnesano, A. Galliani, E. Ippoliti, P. Carloni, G. Natile, Structural biology of cisplatin complexes with cellular targets: the adduct with human copper chaperone Atox1 in aqueous solution, Chemistry A European Journal 2014. 20(37): p. 11719-25.
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42.  Nguyen T. H., G. Rossetti, F. Arnesano, E. Ippoliti, G. Natile, P. Carloni, Molecular recognition of platinated DNA from chromosomal HMGB1, Journal of Chemical Theory and Computation 2014. 10(8): p 3578–3584.
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43.  Calandrini V., F. Arnesano, A. Galliani, T. H. Nguyen, E. Ippoliti, P. Carloni, G. Natile, Platination of the copper transporter ATP7A involved in anticancer drug resistance, Dalton Transactions 2014. 43(31): p. 12085-12094.
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44.  Quy V. C., V. Carnevale, L. Manganaro, M. Lusic, G. Rossetti, V. Leone, C. Fenollar-Ferrer, S. Raugei, G. Del Sal, M. Giacca, P. Carloni, HIV-1 Integrase Binding to its Cellular Partners: A Perspective from Computational Biology, Current Pharmaceutical Design 2014. 20(21): p. 3412-3421.
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45.  Musiani F., G. Rossetti, A. Giorgetti, P. Carloni, Chemosensorial G-proteins-coupled receptors: a perspective from computational methods, Advances in experimental medicine and biology 2014. 805: p. 441-457.
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46.  Kolář M. H., J. Hostaš and P. Hobza, The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole, Physical Chemistry Chemical Physics 2014. 16: p. 9987-9996.
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47.  Papamokos G., J. Dreyer, L. Navarini and P. Carloni, Trapping acrylamide by a Michael addition: A computational study of the reaction between acrylamide and niacin, International Journal of Quantum Chemistry 2014. 114(9): p. 553-559.
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48.  Sandal M., D. Paltrinieri, P. Carloni, F. Musiani, A. Giorgetti, Structure/Function Relationships of Phospholipases C Beta, Current Protein & Peptide Science 2013. 14(8): p. 650-657.
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49.  Zheng W. W., A. V. Vargiu, M. A. Rohrdanz, P. Carloni, C. Clementi, Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile, Journal of Chemical Physics 2013. 139(14): p. 145102.
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50.  Sandal M., T. P. Duy, M. Cona, H. Zung, P. Carloni, F. Musiani, A. Giorgetti, GOMoDo: A GPCRs Online Modeling and Docking Webserver, PLoS ONE 2013. 8: p. e74092.
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51.  Cong X., N. Casiraghi, G. Rossetti, S. Mohanty, G. Giachin, G. Legname, P. Carloni, Role of prion disease-linked mutations in the intrinsically disordered N-terminal domain of the prion protein, Journal of Chemical Theory and Computation 2013. 9 (11): p. 5158–5167
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52.  Dreyer J., P. Strodel, E. Ippoliti, J. Finnerty, R. Eisenberg, P. Carloni, Ion permeation in the NanC Porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations, J. Phys. Chem. B 2013. 117: p. 13534–13542.
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53.  Dibenedetto D., G. Rossetti, R. Caliandro, P. Carloni, A Molecular Dynamics Simulation-Based Interpretation of Nuclear Magnetic Resonance Multidimensional Heteronuclear Spectra of αSynuclein·Dopamine Adducts. Biochemistry 2013. 52: p. 6672-6683.
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54.  Rossetti G., S. Bongarzone, P. Carloni, Computational Studies on the Prion Protein. Current Topics in Medicinal Chemistry 2013. 13: p. 2419-2431.
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55.  Ganesan A., J. Dreyer, F. Wang, J. Akola, J. Larrucea, Density functional study of Cu2+-phenylalanine complex under micro-solvated environment. J. Mol. Graphics Modelling 2013. 113: p. 180-191.
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56.  Cong X., S. Bongarzone, G. Giachin, G. Rossetti, P. Carloni, G. Legname, Dominant-negative effects in prion diseases: insights from molecular dynamics simulations on mouse prion protein chimeras. Journal of Biomolecular Structure & Dynamics 2013. 31(8): p. 829-840.
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57.  Dreyer J., C. Zhang, E. Ippoliti, P. Carloni, Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. Journal of Chemical Theory and Computation 2013.  9(8): p. 3826–3831.
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58.  Marchiori A., L. Capece, A. Giorgetti, P. Gasparini, M.Behrens, P. Carloni, W. Meyerhof, Coarse-Grained/Molecular Mechanics of the TAS2R38 Bitter Taste Receptor: Experimentally-Validated Detailed Structural Prediction of Agonist Binding. PLoS ONE 2013. 8(5): p. e64675.
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59.  Musiani F., E. Ippoliti, C. Micheletti, P. Carloni, S. Ciurli, Conformational Fluctuations of UreG, an Intrinsically Disordered Enzyme. Biochemistry 2013. 52(17): p. 2949-2954.
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60.  Do T. N., P. Carloni, G. Varani, G. Bussi, RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations. Journal of Chemical Theory and Computation 2013. 9(3): p. 1720-1730.
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61.  Mosca Conte A., C. Violante, M. Missori, F. Bechstedt, L. Teodonio, E. Ippoliti, P. Carloni, L. Guidoni, O. Pulci, Theoretical optical spectroscopy of complex systems. Journal of Electron Spectroscopy 2013. 189: p. 46-55.
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62.  Finnerty J. J., R. Eisenberg, P. Carloni, Localizing the Charged Side Chains of Ion Channels within the Crowded Charge Models. Journal of Chemical Theory and Computation 2013. 9(1): p 766-773.
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63.  Gonçalves M.B., J. Dreyer, P. Lupieri, C. Barrera-Patiño, E. Ippoliti, M. R. Webb, J. E. T. Corrie, P. Carloni, Structural prediction of a rhodamine-based biosensor and comparison with biophysical data. Physical Chemistry Chemical Physics 2013. 15: p. 2177–2183.
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64.  Caliandro R., G. Rossetti, P. Carloni, Local Fluctuations and Conformational Transitions in Proteins. Journal of Chemical Theory and Computation 2012. 8(11): p. 4775-4785.
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65.  Marchese R., R. Grandori, P. Carloni, S. Raugei, A Computational Model for Protein Ionization by Electrospray Based on Gas-Phase Basicity. Journal of the American Society for Mass Spectrometry 2012. 23(11): p. 1903-1910.
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66.  Losasso V., S. Schiffer, S. Barth, P. Carloni, Design of human granzyme B variants resistant to serpin B9. Proteins 2012. 80(11): p. 2514-2522.
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67.  Leguebe M., C. Nguyen, L. Capece, Z. Hoang, A. Giorgetti, P. Carloni, Hybrid Molecular Mechanics/Coarse-Grained Simulations for Structural Prediction of G-Protein Coupled Receptor/Ligand Complexes, PLoS ONE 2012. 7(10): p. e47332.
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68.  Quy V. C., S. Pantano, G. Rossetti, M. Giacca, P. Carloni, HIV-1 Tat Binding to PCAF Bromodomain: Structural Determinants from Computational Methods. Biology 2012. 1(2): p. 277-296.
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69.  Nguyen T. H., F. Arnesano, S. Scintilla, G. Rossetti, E. Ippoliti, P. Carloni, G. Natile, Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach. Journal of Chemical Theory and Computation 2012. 8(8): p. 2912-2920.
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70.  Ghaemi Bafghi Z., M. Minozzi, P. Carloni, A. Laio, A Novel Approach to the Investigation of Passive Molecular Permeation through Lipid Bilayers from Atomistic Simulations. Journal of Physical Chemistry B 2012. 116(29): p. 8714-8721.
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71.  Zhang C., D. Knyazev, Y. Vereshchaga, E. Ippoliti, T. H.Nguyen, P. Carloni, P. Pohl, Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion. Proc. Natl. Acad. Sci. USA 2012. 109: p. 9744-9749.
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72.  Fenollar-Ferrer C., C. Anselmi, V. Carnevale, S. Raugei, P. Carloni, Insights on the acetylated NF-kappa B transcription factor complex with DNA from molecular dynamics simulations. Proteins 2012. 80(6): p. 1560-1568.
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73.  Pietropaolo A., P. Carloni, Molecular Simulations of the NGF Protein. In Encyclopedia of Biophysics, Springer-Verlag Berlin Heidelberg, 1590-1593 (2012).
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74.  Sgrignani J., A. Magistrato, M. Dal Peraro, A.J. Villa, P. Carloni, R. Pierattelli, On the active site of mononuclear B1 metallo beta-lactamases: a computational study. Journal of Computer-Aided Molecular Design 2012. 26(4): p. 425-435.
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75.  Ippoliti E., J. Dreyer, P. Carloni, U. Röthlisberger, Hybrid Car-Parrinello Molecular Dynamics / Molecular Mechanics Simulations: A Powerful Tool for the Investigation of Biological Systems. In “Hierarchical Methods for Dynamics in Complex Molecular Systems” edited by J. Grotendorst, G. Sutmann, G. Gompper, D. Marx, IAS Series Vol. 10, 163-181 (2012).
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76.  Giorgetti A., P. Ruggerone, S. Pantano, and P. Carloni, Advanced Computational Methods in Molecular Medicine. Journal of Biomedicine and Biotechnology 2012. 2012: p. 709085.
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77.  Zhang C., P. Carloni, Salt effects on water/hydrophobic liquid interfaces: a molecular dynamics study. Journal Phys-Cond. Matter 2012. 24(12): p. 124109.
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78.  Do N. T., E. Ippoliti, P. Carloni, G. Varani, M. Parrinello, Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. Journal of Chemical Theory and Computation 2012. 8(2): p. 688-694.
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79.  Chiriano G., A. De Simone, F. Mancini, D. I. Perez, A. Cavalli, M. L. Bolognesi, G. Legname, A. Martinez, V. Andrisano, P. Carloni, M. Roberti, A small chemical library of 2-aminoimidazole derivatives as BACE-1 inhibitors: Structure-based design, synthesis, and biological evaluation. European Journal of Medicinal Chemistry 2012. 48: p. 206-213.
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80.  Rossetti G., P. Cossio, A. Laio, P. Carloni, Conformations of the Huntingtin N-term in aqueous solution from atomistic simulations. FEBS Letters 2011. 585(19): p. 3086-3089.
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81.  Giorgetti A., S. Piccoli, Knowledge Based Membrane Protein Structure Prediction: From X-Ray Crystallography to Bioinformatics and Back to Molecular Biology, in Current Trends in X-Ray Crystallography, edited by Annamalai Chandrasekaran, InTech Publisher (2011).
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82.  Modena D., M. Trentini, M. Corsini, A. Bombaci, A. Giorgetti, OlfactionDB: A Database of Olfactory Receptors and Their Ligands. Advances in Life Sciences 2011. 1(1): p. 9-13.
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83.  Zanzoni S., M. Assfalg, A. Giorgetti, M. D'Onofrio, H. Molinari, Structural Requirements for Cooperativity in Ileal Bile Acid-binding Proteins. Journal of Biological Chemistry 2011. 286(45): p. 39307-17.
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84.  Lima E., P. Carloni, Acrylamide Binding to Its Cellular Targets: Insights from Computational Studies, in Computational Biology and Applied Bioinformatics, edited by H.S. Lops and L.M. Cruz, InTech Publisher (2011).
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85.  Rossetti G., X. Cong, R. Caliandro, G. Legname, P. Carloni, Common Structural Traits across Pathogenic Mutants of the Human Prion Protein and Their Implications for Familial Prion Diseases. Journal of Molecular Biology 2011. 411(3): p. 700-712.
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86.  Losasso, V., A. Pietropaolo, C. Zannoni, S. Gustincich, P. Carloni, Structural Role of Compensatory Amino Acid Replacements in the alpha-Synuclein Protein. Biochemistry 2011. 50(32): p. 6994-7001.
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87.  Minozzi M., G. Lattanzi, R. Benz, M.P. Costi, A. Venturelli, P. Carloni, Permeation through the Cell Membrane of a Boron-Based beta-Lactamase Inhibitor. PLoS ONE  2011. 6(8): p. e23187.
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88.  Biarnés X., Bongarzone S., Vargiu A.V., Carloni P., Ruggerone P., Molecular motions in drug design: the coming age of the metadynamics method. Journal of Computer-Aided Molecular Design 2011. 25(5): p. 395-402.
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89.  Bongarzone S., H. N. A. Tran, A. Cavalli, M. Roberti, M. Rosini, P. Carloni, G. Legname, M. L. Bolognesi, Hybrid Lipoic Acid Derivatives to Attack Prion Disease on Multiple Fronts. ChemMedChem  2011. 6(4) Special Issue: p. 601-605.
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90.  Chiriano G., A. Sartini,  F. Mancini, V. Andrisano, M. L. Bolognesi, M. Roberti, M. Recanatini, P. Carloni, A. Cavalli, Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE-1 Inhibitors. Chemical Biology & Drug Design 2011. 77(4): p. 268-271.
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91.  Bongarzone S., H. N. A. Tran, A. Cavalli, M. Roberti, P. Carloni, G. Legname, M. L. Bolognesi, Parallel Synthesis, Evaluation, and Preliminary Structure-Activity Relationship of 2,5-Diamino-1,4-benzoquinones as a Novel Class of Bivalent Anti-Prion Compound. Journal of Medicinal Chemistry 2010. 53: p. 8197-8201.
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92.  Binolfi A., E. E. Rodriguez, D. Valensin, N. D’Amelio, E. Ippoliti, G. Obal, R. Duran, A. Magistrato, O. Pritsch, M. Zweckstetter,G. Valensin, P. Carloni, L. Quintanar, C. Griesinger, C. O. Fernandez, Bioinorganic Chemistry of Parkinson’s Disease: Structural Determinants for the Copper-Mediated Amyloid Formation of Alpha-Synuclein. Inorganic Chemistry 2010. 49: p. 10668-10679.
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93.  Rossetti G., G. Giachin, G. Legname, P. Carloni, Structural Facets of Disease-Linked Human Prion Protein Mutants: A Molecular Dynamic Study. Protein-Structure Function and Bioinformatics 2010. 78(16): p. 3270-3280.
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94.  Musiani F., B. Bertosa, A. Magistrato, B. Zambelli, P. Turano, V. Losasso, C. Micheletti, S. Ciurli, P. Carloni, Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+. Journal of Chemical Theory and Computation 2010. 6(11): p. 3503-3515.
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95.  Lupieri P., E. Ippoliti, P. Altoè, M. Garavelli, M. Mwalaba, P. Carloni, Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car-Parrinello and TDDFT/CASPT2 Calculations. Journal of Chemical Theory and Computation 2010. 6(11): p. 3403-3409.
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96.  Biarnés X., A. Marchiori, A. Giorgetti, C. Lanzara, P. Gasparin, P. Carloni, S. Born, A. Brockhoff, M. Behrens, M. Meyerhof, Insights into the Binding of Phenyltiocarbamide (PTC) Agonist to Its Target Human TAS2R38 Bitter Receptor, 2010. PLoS ONE 5(8): p. e12394.
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97.  Bolognesi M. L., H. N. A. Tran, M. Staderini, A. Monac, A. Lopez-Cobenas, S. Bongarzone, X. Biarnés, P. Lopez-Alvarado, N. Cabezas, M. Caramelli, P. Carloni, J. C. Menendez, G. Legname, Discovery of a Class of Diketopiperazines as Antiprion Compounds. ChemMedChem 2010. 5(8): p. 1157.
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98.  Zhang C., S. Raugei, B. Eisenberg, P. Carloni, Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength. Journal of Chemical Theory and Computation 2010. 6(7): p. 2167-2175.
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99.  Dal Peraro M., A. J. Vila, P. Carloni, Catalytic Mechanism of Metallo β‐Lactamases: Insights from Calculations and Experiments. In Quantum Biochemistry edited by C. F. Matta: p. 605-622 (2010).
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100.  Marchese R., R. Grandori, P. Carloni, S. Raugei, On the Zwitterionic Nature of Gas-Phase Peptides and Protein Ions. PLOS Computational Biology 2010. 6(5): p. e1000775.
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101.  Rossetti G., A. Magistrato, A. Pastore, P. Carloni, Hydrogen Bonding Cooperativity in polyQ β-Sheets from First Principle Calculations. Journal of Chemical Theory and Computation, 2010. 6(5): p. 1777-1782.
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102.  Leone, V., F. Marinelli, P. Carloni, M. Parrinello, Targeting biomolecular flexibility with metadynamics. Current Opinion in Structural Biology, 2010. 20(2): p. 148-154.
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103.  Bucher, D., L. Guidoni, P. Carloni, U. Röthlisberger. Coordination Numbers of K+ and Na+ Ions Inside the Selectivity Filter of the KcsA Potassium Channel: Insights from First Principles Molecular Dynamics. Biophysical Journal, 2010. 98 (10): p. L47-L49.
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104.  Robertazzi A., A. Magistrato, M. Dal Peraro, P. Carloni, First Principles DFT Studies of Metal-Based Biological and Biomimetic Systems. In Metallic Systems: A Quantum Chemists Perspective edited by T. C. Allison, O. Coskuner, C. A. González. 2010: p. 1-28.
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105.  Griguoli M., A. Maul, C. Nguyen, A. Giorgetti, P. Carloni, E. Cherubini, Nicotine Blocks the Hyperpolarization-Activated Current I-h and Severely Impairs the Oscillatory Behavior of Oriens-Lacunosum Moleculare Interneurons. Journal of  Neuroscience 2010. 30(32):  p. 10773-10783.

106.  Mosca Conte, A., E. Ippoliti, R. Del Sole, P. Carloni, O. Pulci, Many-body meets QM/MM: Application to indole in water solution. Physica Status Solidi B – Basic Solid State Physics, 2010. 247(8): p. 1920-1924.

107.  Munoz-Lopez F.J., S. Raugei, M.A. De la Rosa, A.J. Diaz-Quintana, P. Carloni, Changes in non-core regions stabilise plastocyanin from the thermophilic cyanobacterium Phormidium laminosum. Journal of Biological Inorganic Chemistry 2010. 15(3): p. 329-338.

108.  Tran H.N.A., S. Bongarzone, P. Carloni, G. Legname, M.L. Bolognesi, Synthesis and evaluation of a library of 2,5-bisdiamino-benzoquinone derivatives as probes to modulate protein-protein interactions in prions. Bioorganic & Medicinal Chemistry Letters 2010. 20(6): p.1866-1868.

109.  Latawiec D., F. Herrera, A. Bek, V. Losasso, M. Candotti, F. B. E. Carlino, A. Kranjc, M. Lazzarino, S. Gustincich, P. Carloni, G. Legname, Modulation of Alpha-Synuclein Aggregation by Dopamine Analogs. PLoS ONE, 2010. 5(2): p. e9234.

110.  Kranjc A., F.W. Grillo, J. Rievaj, A. Boccaccio, F. Pietrucci, A. Menini, P. Carloni, C. Anselmi, Regulation Bestrophins by Ca2+: A Theoretical and Experimental Study. PLoS ONE, 2009. 4(3): p. e4672.

111.  Simona F., A. Magistrato, M. Dal Peraro, A. Cavalli, A.J. Vila, and P. Carloni, Common Mechanistic Features among Metallo-beta-lactamases - A Computational Study Of Aeromonas Hydrophila Cpha Enzyme. Journal of Biological Chemistry, 2009. 284(41): p. 28164-28171.

112.  Robertazzi A., A.V. Vargiu, A. Magistrato, P. Ruggerone, P. Carloni, P. de Hoog, and J. Reedijk, Copper-1,10-Phenanthroline Complexes Binding to DNA: Structural Predictions from Molecular Simulations. Journal of Physical Chemistry B, 2009. 113(31): p. 10881-10890.

113.  Pietrucci F., F. Marinelli, P. Carloni, and A. Laio, Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations. Journal of the American Chemical Society, 2009. 131(33): p. 11811-11818.

114.  Lupieri P., C.H.H. Nguyen, Z.G. Bafghi, A. Giorgetti, and P. Carloni, Computational molecular biology approaches to ligand-target interactions. Hfsp Journal, 2009. 3(4): p. 228-239.

115.  Liu H.Y., C. Fenollar-Ferrer, A.Q. Cao, C. Anselmi, P. Carloni, and J.W. Liu, Molecular dissection of human oncostatin M-mediated signal transductions through site-directed mutagenesis. International Journal of Molecular Medicine, 2009. 23(2): p. 161-172.

116.  Leone V., G. Lattanzi, C. Molteni, and P. Carloni, Mechanism of Action of Cyclophilin A Explored by Metadynamics Simulations. PLOS Computational Biology, 2009. 5(3): p. e1000309.

117.  Mosca Conte A., V. Garbuio, M. Marsili, E. Ippoliti, R. Del Sole, P. Carloni, O. Pulci, Excited-state properties calculations: Applications to biological systems. Nuovo Cimento della Societá Italiana di Fisica C - Colloquia on Physics, 2009. 32(2): p. 73-76.

118.  Kranjc A., S. Bongarzone, G. Rossetti, X. Biarnés, A. Cavalli, M.L. Bolognesi, M. Roberti, G. Legname, and P. Carloni, Docking Ligands on Protein Surfaces: The Case Study of Prion Protein. Journal of Chemical Theory and Computation, 2009. 5(9): p. 2565-2573.

119.  Khafizov K., G. Lattanzi, and P. Carloni, G protein inactive and active forms investigated by simulation methods. Proteins-Structure Function and Bioinformatics, 2009. 75(4): p. 919-930.

120.  D'Arco M., R. Giniatullin, V. Leone, P. Carloni, N. Birsa, A. Nair, A. Nistri, and E. Fabbretti, The C-terminal Src Inhibitory Kinase (Csk)-mediated Tyrosine Phosphorylation Is a Novel Molecular Mechanism to Limit P2X(3) Receptor Function in Mouse Sensory Neurons. Journal of Biological Chemistry, 2009. 284(32): p. 21393-21401.

121.  Mosca Conte A., E. Ippoliti, R. Del Sole, P. Carloni, and O. Pulci, Many-Body Perturbation Theory Extended to the Quantum Mechanics/Molecular Mechanics Approach: Application to Indole in Water Solution. Journal of Chemical Theory and Computation, 2009. 5(7): p. 1822-1828.

122.  Carnevale V., S. Raugei, M. Neri, S. Pantano, C. Micheletti, and P. Carloni, Multi-scale modeling of HIV-1 proteins. Journal of Molecular Structure-Theochem, 2009. 898(1-3): p. 97-105.

123.  Vargiu A.V., P. Ruggerone, A. Magistrato, and P. Carloni, Sliding of alkylating anticancer drugs along the minor groove of DNA: New insights on sequence selectivity. Biophysical Journal, 2008. 94(2): p. 550-561.

124.  Herrera F.E., A. Chesi, K.E. Paleologou, A. Schmid, A. Munoz, M. Vendruscolo, S. Gustincich, H.A. Lashuel, P. Carloni, Inhibition of alpha-Synuclein Fibrillization by Dopamine Is Mediated by Interactions with Five C-Terminal Residues and with E83 in the NAC Region. PLoS ONE, 2008. 3(10).

125.  Vargiu A.V., P. Ruggerone, A. Magistrato, and P. Carloni, Dissociation of minor groove binders from DNA: insights from metadynamics simulations. Nucleic Acids Research, 2008. 36(18): p. 5910-5921.

126.  Vargiu A.V., A. Robertazzi, A. Magistrato, P. Ruggerone, and P. Carloni, The hydrolysis mechanism of the anticancer ruthenium drugs NAMI-A and ICR investigated by DFT-PCM calculations. Journal of Physical Chemistry B, 2008. 112(14): p. 4401-4409.

127.  Tomatis P.E., S.M. Fabiane, F. Simona, P. Carloni, B.J. Sutton, and A.J. Vila, Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proceedings of the National Academy of Sciences of the United States of America, 2008. 105(52): p. 20605-20610.

128.  Spiegel K., A. Magistrato, P. Maurer, P. Ruggerone, U. Röthlisberger, P. Carloni, J. Reedijk, and M.L. Klein, Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure. Journal of Computational Chemistry, 2008. 29(1): p. 38-49.

129.  Rossetti G., A. Magistrato, A. Pastore, F. Persichetti, and P. Carloni, Structural Properties of Polyglutamine Aggregates Investigated via Molecular Dynamics Simulations. Journal of Physical Chemistry B, 2008. 112(51): p. 16843-16850.

130.  Otyepka M., P. Banas, A. Magistrato, P. Carloni, and J. Damborsky, Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins-Structure Function and Bioinformatics, 2008. 70(3): p. 707-717.

131.  Neri M., M. Baaden, V. Carnevale, C. Anselmi, A. Maritan, and P. Carloni, Microseconds dynamics simulations of the outer-membrane protease T. Biophysical Journal, 2008. 94(1): p. 71-78.

132.  Hong R., A. Magistrato, and P. Carloni, Anthrax Lethal Factor Investigated by Molecular Simulations. Journal of Chemical Theory and Computation, 2008. 4(10): p. 1745-1756.

133.  Guida E., A. Bisso, C. Fenollar-Ferrer, M. Napoli, C. Anselmi, J.E. Girardini, P. Carloni, and G. Del Sal, Peptide aptamers targeting mutant p53 induce apoptosis in tumor cells. Cancer Research, 2008. 68(16): p. 6550-6558.

134.  Fenollar-Ferrer C., V. Carnevale, S. Raugei, and P. Carloni, HIV-1 integrase-DNA interactions investigated by molecular modelling. Computational and Mathematical Methods in Medicine, 2008. 9(3-4): p. 231-243.

135.  Cascella M., M.A. Neri, P. Carloni, and M. Dal Peraro, Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins. Journal of Chemical Theory and Computation, 2008. 4(8): p. 1378-1385.

136.  Carnevale V., S. Raugei, S. Piana, P. Carloni, On the nature of the reaction intermediate in the HIV-1 protease: a quantum chemical study. Computer Physics Communications, 2008. 179(1-3): p. 120-123.

137.  Sulpizi M., S. Raugei, J. VandeVondele, P. Carloni, and M. Sprik, Calculation of redox properties: Understanding short- and long-range effects in rubredoxin. Journal of Physical Chemistry B, 2007. 111(15): p. 3969-3976.

138.  Spiegel K., A. Magistrato, P. Carloni, J. Reedijk, and M.L. Klein, Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance. Journal of Physical Chemistry B, 2007. 111(41): p. 11873-11876.

139.  Simona F., A. Magistrato, D.M.A. Vera, G. Garau, A.J. Vila, and P. Carloni, Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila. Proteins-Structure Function and Bioinformatics, 2007. 69(3): p. 595-605.

140.  Robertazzi A., A. Magistrato, P. de Hoog, P. Carloni, and J. Reedijk, Density functional theory studies on copper phenanthroline complexes. Inorganic Chemistry, 2007. 46(15): p. 5873-5881.

141.  Kranjc A., C. Anselmi, P. Carloni, F.E. Blaney, Structural models of human big conductance calcium- and voltage-gated potassium channels. Computer Physics Communications, 2007. 177(1-2): p. 21-26.

142.  Moran-Barrio J., J.M. Gonzalez, M.N. Lisa, A.L. Costello, M. Dal Peraro, P. Carloni, B. Bennett, D.L. Tierney, A.S. Limansky, A.M. Viale, and A.J. Vila, The metallo-ss-lactamase GOB is a mono-Zn(II) enzyme with a novel active site. Journal of Biological Chemistry, 2007. 282(25): p. 18286-18293.

143.  Miani A., S. Raugei, P. Carloni, and M.S. Helfand, Structure and Raman spectrum of clavulanic acid in aqueous solution. Journal of Physical Chemistry B, 2007. 111(10): p. 2621-2630.

144.  Magistrato A., A. Robertazzi, and P. Carloni, Nitrogen fixation by a molybdenum catalyst mimicking the function of the nitrogenase enzyme: A critical evaluation of DFT and solvent effects. Journal of Chemical Theory and Computation, 2007. 3(5): p. 1708-1720.

145.  Kona J., M. Minozzi, V. Torre, and P. Carloni, A gate mechanism indicated in the selectivity filter of the potassium channel KscA. Theoretical Chemistry Accounts, 2007. 117(5-6): p. 1121-1129.

146.  Khafizov K., C. Anselmi, A. Menini, and P. Carloni, Ligand specificity of odorant receptors. Journal of Molecular Modeling, 2007. 13(3): p. 401-409.

147.  Herrera F.E., S. Zucchelli, A. Jezierska, Z.S. Lavina, S. Gustincich, and P. Carloni, On the oligomeric state of DJ-1 protein and its mutants associated with Parkinson disease - A combined computational and in vitro study. Journal of Biological Chemistry, 2007. 282(34): p. 24905-24914.

148.  De Vivo M., A. Cavalli, P. Carloni, and M. Recanatini, Computational study of the phosphoryl transfer catalyzed by a cyclin-dependent kinase. Chemistry-a European Journal, 2007. 13(30): p. 8437-8444.

149.  Dal Peraro M., A.J. Vila, P. Carloni, and M.L. Klein, Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases. Journal of the American Chemical Society, 2007. 129(10): p. 2808-2816.

150.  Dal Peraro M., P. Ruggerone, S. Raugei, F.L. Gervasio, and P. Carloni, Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Current Opinion in Structural Biology, 2007. 17(2): p. 149-156.

151.  Carnevale V., S. Raugei, C. Micheletti, and P. Carloni, Large-scale motions and electrostatic properties of furin and HIV-1 protease. Journal of Physical Chemistry A, 2007. 111(49): p. 12327-12332.

152.  Berrera M., S. Pantano, and P. Carloni, Catabolite activator protein in aqueous solution: A molecular simulation study. Journal of Physical Chemistry B, 2007. 111(6): p. 1496-1501.

153.  Anselmi C., P. Carloni, and V. Torre, Origin of functional diversity among tetrameric voltage-gated channels. Proteins-Structure Function and Bioinformatics, 2007. 66(1): p. 136-146.

154.  Vidossich P., S. Piana, A. Miani, and P. Carloni, Deuterium isotope effects in A : T and A : U base pairs: A computational NMR study. Journal of the American Chemical Society, 2006. 128(22): p. 7215-7221.

155.  Vidossich P. and P. Carloni, Binding of phosphinate and phosphonate inhibitors to aspartic proteases: A first-principles study. Journal of Physical Chemistry B, 2006. 110(3): p. 1437-1442.

156.  Vargiu A.V., P. Ruggerone, A. Magistrato, and P. Carloni, Anthramycin-DNA binding explored by molecular simulations. Journal of Physical Chemistry B, 2006. 110(48): p. 24687-24695.

157.  Bucher D., S. Raugei, L. Guidoni, M. Dal Peraro, U. Röthlisberger, P. Carloni, M.L. Klein, Polarization effects and charge transfer in the KcsA potassium channel. Biophysical Chemistry, 2006. 124(3): p. 292-301.

158.  Spiegel K., U. Röthlisberger, and P. Carloni, Duocarmycins binding to DNA investigated by molecular simulation. Journal of Physical Chemistry B, 2006. 110(8): p. 3647-3660.

159.  Raugei S., F.L. Gervasio, and P. Carloni, DFT modeling of biological systems. Physica Status Solidi B-Basic Solid State Physics, 2006. 243(11): p. 2500-2515.

160.  Raugei S. and P. Carloni, Structure and function of vanadium haloperoxidases. Journal of Physical Chemistry B, 2006. 110(8): p. 3747-3758.

161.  Pantano S., A. Marcello, A. Ferrari, D. Gaudiosi, A. Sabo, V. Pellegrini, F. Beltram, M. Giacca, and P. Carloni, Insights on HIV-1 Tat : P/CAF bromodomain molecular recognition from in vivo experiments and molecular dynamics simulations. Proteins-Structure Function and Bioinformatics, 2006. 62(4): p. 1062-1073.

162.  Miani A., P. Carloni, and S. Raugei, A novel parametrization scheme for classical and quantum mechanical simulations of large, floppy molecular systems. Chemical Physics Letters, 2006. 427(1-3): p. 230-235.

163.  Magistrato A., P. Ruggerone, K. Spiegel, P. Carloni, and J. Reedijk, Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: Insights from hybrid QM/MM molecular dynamics simulations. Journal of Physical Chemistry B, 2006. 110(8): p. 3604-3613.

164.  Fiorin G., A. Pastore, P. Carloni, and M. Parrinello, Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail. Biophysical Journal, 2006. 91(8): p. 2768-2777.

165.  Cavallari M., C. Ghio, S. Monti, M. Ferrario, A. Maritan, P. Carloni, Partially folded states of HIV-1 protease: Molecular dynamics simulations and ligand binding. Journal of Molecular Structure-Theochem, 2006. 769(1-3): p. 111-121.

166.  De Vivo M., A. Cavalli, G. Bottegoni, P. Carloni, and M. Recanatini, Role of phosphorylated Thr160 for the activation of the CDK2/Cyclin a complex. Proteins-Structure Function and Bioinformatics, 2006. 62(1): p. 89-98.

167.  Cavalli A., P. Carloni, and M. Recanatini, Target-related applications of first principles quantum chemical methods in drug design. Chemical Reviews, 2006. 106(9): p. 3497-3519.

168.  Cascella M., A. Magistrato, I. Tavernelli, P. Carloni, and U. Röthlisberger, Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa. Proceedings of the National Academy of Sciences of the United States of America, 2006. 103(52): p. 19641-19646.

169.  Carnevale V., S. Raugei, C. Micheletti, and P. Carloni, Convergent dynamics in the protease enzymatic superfamily. Journal of the American Chemical Society, 2006. 128(30): p. 9766-9772.

170.  Berrera M., S. Pantano, and P. Carloni, CAMP modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations. Biophysical Journal, 2006. 90(10): p. 3428-3433.

171.  Neri M., C. Anselmi, V. Carnevale, A. V. Vargiu, P. Carloni, Molecular dynamics simulations of outer-membrane protease T from E-coli based on a hybrid coarse-grained/atomistic potential, J. Phys.: Cond. Mat., 2006. 18(14): p. S347-S355.

172.  Berrera M., A. Cattaneo, and P. Carloni, Molecular simulation of the binding of nerve growth factor peptide mimics to the receptor tyrosine kinase A. Biophysical Journal, 2006. 91(6): p. 2063-2071.

173.  Pantano S., M. Zaccolo, and P. Carloni, Molecular basis of the allosteric mechanism of cAMP in the regulatory PKA subunit. Febs Letters, 2005. 579(12): p. 2679-2685.

174.  Pantano S. and P. Carloni, Comparative analysis of HIV-1 Tat variants. Proteins-Structure Function and Bioinformatics, 2005. 58(3): p. 638-643.

175.  Neri M., C. Anselmi, M. Cascella, A. Maritan, and P. Carloni, Coarse-grained model of proteins incorporating atomistic detail of the active site. Physical Review Letters, 2005. 95(21).

176.  Giorgetti A., A.V. Nair, P. Codega, V. Torre, and P. Carloni, Structural basis of gating of CNG channels. Febs Letters, 2005. 579(9): p. 1968-1972.

177.  Giorgetti A., P. Carloni, P. Mistrik, and V. Torre, A homology model of the pore region of HCN channels. Biophysical Journal, 2005. 89(2): p. 932-944.

178.  Fiorin G., R.R. Biekofsky, A. Pastore, and P. Carloni, Unwinding the helical linker of calcium-loaded calmodulin: A molecular dynamics study. Proteins-Structure Function and Bioinformatics, 2005. 61(4): p. 829-839.

179.  Dal Peraro M., S. Raugei, P. Carloni, and M.L. Klein, Solute-solvent charge transfer in aqueous solution. Chemphyschem, 2005. 6(9): p. 1715-1718.

180.  Cascella M., C. Micheletti, U. Röthlisberger, and P. Carloni, Evolutionarily conserved functional mechanics across pepsin-like and retroviral aspartic proteases. Journal of the American Chemical Society, 2005. 127(11): p. 3734-3742.

181.  Vidossich P., M. Cascella, and P. Carloni, Dynamics and energetics of water permeation through the aquaporin channel. Proteins-Structure Function and Bioinformatics, 2004. 55(4): p. 924-931.

182.  Spiegel K., U. Röthlisberger, and P. Carloni, Cisplatin binding to DNA oligomers from hybrid Car-Parrinello/molecular dynamics simulations. Journal of Physical Chemistry B, 2004. 108(8): p. 2699-2707.

183.  Raugei S., M. Cascella, and P. Carloni, A proficient enzyme: Insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. Journal of the American Chemical Society, 2004. 126(48): p. 15730-15737.

184.  Piana S., D. Bucher, P. Carloni, and U. Röthlisberger, Reaction mechanism of HIV-1 protease by hybrid carparrinello/classical MD simulations. Journal of Physical Chemistry B, 2004. 108(30): p. 11139-11149.

185.  Pantano S., M. Tyagi, M. Giacca, and P. Carloni, Molecular dynamics simulations on HIV-1 Tat. European Biophysics Journal with Biophysics Letters, 2004. 33(4): p. 344-351.

186.  Musiani F., P. Carloni, and S. Ciurli, The asn 38-cys 84 H-bond in plastocyanin. Journal of Physical Chemistry B, 2004. 108(22): p. 7495-7499.

187.  Micheletti C., P. Carloni, and A. Maritan, Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models. Proteins-Structure Function and Bioinformatics, 2004. 55(3): p. 635-645.

188.  Dal Peraro M., A.J. Vila, and P. Carloni, Substrate binding to mononuclear metallo-beta-lactamase from Bacillus cereus. Proteins-Structure Function and Genetics, 2004. 54(3): p. 412-423.

189.  Dal Peraro M., L.I. Llarrull, U. Röthlisberger, A.J. Vila, and P. Carloni, Water-assisted reaction mechanism of monozinc beta-lactamases. Journal of the American Chemical Society, 2004. 126(39): p. 12661-12668.

190.  Compoint M., P. Carloni, C. Ramseyer, and C. Girardet, Molecular dynamics study of the KcsA channel at 2.0-angstrom resolution: stability and concerted motions within the pore. Biochimica Et Biophysica Acta-Biomembranes, 2004. 1661(1): p. 26-39.

191.  Cascella M., S. Raugei, and P. Carloni, Formamide hydrolysis investigated by multiple-steering ab initio molecular dynamics. Journal of Physical Chemistry B, 2004. 108(1): p. 369-375.

192.  Sulpizi M., U. Röthlisberger, and P. Carloni, Molecular dynamics studies of caspase-3. Biophysical Journal, 2003. 84(4): p. 2207-2215.

193.  Sulpizi M., A. Laio, J. VandeVondele, A. Cattaneo, U. Röthlisberger, and P. Carloni, Reaction mechanism of caspases: Insights from QM/MM Car-Parrinello simulations. Proteins-Structure Function and Genetics, 2003. 52(2): p. 212-224.

194.  Sulpizi M., P. Carloni, J. Hutter, and U. Röthlisberger, A hybrid TDDFT/MM investigation of the optical properties of aminocoumarins in water and acetonitrile solution. Physical Chemistry Chemical Physics, 2003. 5(21): p. 4798-4805.

195.  Spiegel K. and P. Carloni, Electrostatic role of phosphate 2485 in the large ribosomal unit from H-marismortui. Journal of Physical Chemistry B, 2003. 107(9): p. 2091-2097.

196.  Settanni G., A. Cattaneo, and P. Carloni, Molecular dynamics simulations of the NGF-TrkA domain 5 complex and comparison with biological data. Biophysical Journal, 2003. 84(4): p. 2282-2292.

197.  Punta M., A. Cavalli, V. Torre, and P. Carloni, Molecular Modeling studies on CNG channel from bovine retinal rod: A structural model of the cyclic nucleotide-binding domain. Proteins-Structure Function and Genetics, 2003. 52(3): p. 332-338.

198.  Giorgetti A. and P. Carloni, Molecular modeling of ion channels: structural predictions. Current Opinion in Chemical Biology, 2003. 7(1): p. 150-156.

199.  Gervasio F.L., V. Schettino, S. Mangani, M. Krack, P. Carloni, and M. Parrinello, Influence of outer-shell metal ligands on the structural and electronic properties of horse liver alcohol dehydrogenase zinc active site. Journal of Physical Chemistry B, 2003. 107(28): p. 6886-6892.

200.  Dal Peraro M., A.J. Vila, and P. Carloni, Protonation state of Asp120 in the binuclear active site of the metallo-beta-lactamase from Bacteroides fragilis. Inorganic Chemistry, 2003. 42(14): p. 4245-4247.

201.  Costa V., A. Nistri, A. Cavalli, and P. Carloni, A structural model of agonist binding to the alpha 3 beta 4 neuronal nicotinic receptor. British Journal of Pharmacology, 2003. 140(5): p. 921-931.

202.  Costa V. and P. Carloni, Calcium, binding to the transmembrane domain of the sarcoplasmic reticulum Ca2+-ATPase: Insights from molecular modeling. Proteins-Structure Function and Genetics, 2003. 50(1): p. 104-113.

203.  Sulpizi M., G. Folkers, U. Röthlisberger, P. Carloni, and L. Scapozza, Applications of density functional theory-based methods in medicinal chemistry. Quantitative Structure-Activity Relationships, 2002. 21(2): p. 173-181.

204.  Piana S., P. Carloni, and U. Röthlisberger, Drug resistance in HIV-1 protease: Flexibility-assisted mechanism of compensatory mutations. Protein Science, 2002. 11(10): p. 2393-2402.

205.  Guidoni L. and Carloni, P., Tetraethylammonium binding to the outer mouth of the KcsA potassium channel: Implications for ion permeation. Journal of Receptor and Signal Transduction Research 2002. 22(1-4): p. 315.

206.  Piana S., P. Carloni, and M. Parrinello, Role of conformational fluctuations in the enzymatic reaction of HIV-1 protease. Journal of Molecular Biology, 2002. 319(2): p. 567-583.

207.  Pantano S., M. Tyagi, M. Giacca, and P. Carloni, Amino acid modification in the HIV-1 Tat basic domain: Insights from molecular dynamics and in vivo functional studies. Journal of Molecular Biology, 2002. 318(5): p. 1331-1339.

208.  Pantano S., F. Alber, D. Lamba, and P. Carloni, NADH interactions with WT- and S94A-acyl carrier protein reductase from Mycobacterium tuberculosis: An ab initio study. Proteins-Structure Function and Genetics, 2002. 47(1): p. 62-68.

209.  Guidoni L. and P. Carloni, Potassium permeation through the KcsA channel: a density functional study. Biochimica Et Biophysica Acta-Biomembranes, 2002. 1563(1-2): p. 1-6.

210.  Gervasio F.L., P. Carloni, and M. Parrinello, Electronic structure of wet DNA. Physical Review Letters, 2002. 89(10).

211.  Di Angelantonio S., V. Costa, P. Carloni, L. Messori, and A. Nistri, A novel class of peptides with facilitating action on neuronal nicotinic receptors of rat chromaffin cells in vitro: Functional and molecular dynamics studies. Molecular Pharmacology, 2002. 61(1): p. 43-54.

212.  Dal Peraro M., A.J. Vila, and P. Carloni, Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site. Journal of Biological Inorganic Chemistry, 2002. 7(7-8): p. 704-712.

213.  Cavalli A. and P. Carloni, Enzymatic GTP hydrolysis: Insights from an ab initio molecular dynamics study. Journal of the American Chemical Society, 2002. 124(14): p. 3763-3768.

214.  Cascella M., L. Guidoni, A. Maritan, U. Röthlisberger, and P. Carloni, Multiple steering molecular dynamics applied to water exchange at alkali ions. Journal of Physical Chemistry B, 2002. 106(50): p. 13027-13032.

215.  Carloni P., U. Röthlisberger, and M. Parrinello, The role and perspective of ab initio molecular dynamics in the study of biological systems. Accounts of Chemical Research, 2002. 35(6): p. 455-464.

216.  Carloni P., Density functional theory-based molecular dynamics of biological systems. Quantitative Structure-Activity Relationships, 2002. 21(2): p. 166-172.

217.  Sulpizi M., P. Schelling, G. Folkers, P. Carloni, and L. Scapozza, The rational of catalytic activity of herpes simplex virus thymidine kinase - A combined biochemical and quantum chemical study. Journal of Biological Chemistry, 2001. 276(24): p. 21692-21697.

218.  Piana S., D. Sebastiani, P. Carloni, and M. Parrinello, Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site. Journal of the American Chemical Society, 2001. 123(36): p. 8730-8737.

219.  Frigyes D., F. Alber, S. Pongor, and P. Carloni, Arginine-phosphate salt bridges in protein-DNA complexes: a Car-Parrinello study. Journal of Molecular Structure-Theochem, 2001. 574: p. 39-45.

220.  Dal Peraro M., F. Alber, and P. Carloni, Ser133 phosphate-KIX interactions in the CREB-CBP complex: an ab initio molecular dynamics study. European Biophysics Journal with Biophysics Letters, 2001. 30(1): p. 75-81.

221.  Cecconi F., C. Micheletti, P. Carloni, and A. Maritan, Molecular dynamics studies on HIV-1 protease drug resistance and folding pathways. Proteins-Structure Function and Genetics, 2001. 43(4): p. 365-372.

222.  Sulpizi M. and P. Carloni, Cation-pi versus OH-pi interactions in proteins: A density functional study. Journal of Physical Chemistry B, 2000. 104(43): p. 10087-10091.

223.  Sigel H., A. Saha, N. Saha, P. Carloni, L.E. Kapinos, and R. Griesser, Evaluation of intramolecular equilibria in complexes formed between substituted imidazole ligands and nickel(II), copper(II) or zinc(II). Journal of Inorganic Biochemistry, 2000. 78(2): p. 129-137.

224.  Röthlisberger U., P. Carloni, K. Doclo, and M. Parrinello, A comparative study of galactose oxidase and active site analogs based on QM/MM Car Parrinello simulations. Journal of Biological Inorganic Chemistry, 2000. 5(2): p. 236-250.

225.  Piana S. and P. Carloni, Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: an ab initio study on the free enzyme. Proteins-Structure Function and Genetics, 2000. 39(1): p. 26-36.

226.  Pantano S., F. Alber, and P. Carloni, Proton dynamics in an enzyme model substrate: an ab initio molecular dynamics study. Journal of Molecular Structure-Theochem, 2000. 530(1-2): p. 177-181.

227.  Guidoni L., V. Torre, and P. Carloni, Water and potassium dynamics inside the KcsA K+ channel. Febs Letters, 2000. 477(1-2): p. 37-42.

228.  Carloni P., M. Sprik, and W. Andreoni, Key steps of the cis-platin-DNA interaction: Density functional theory-based molecular dynamics simulations. Journal of Physical Chemistry B, 2000. 104(4): p. 823-835.

229.  Alber F. and P. Carloni, Ab initio molecular dynamics studies on HIV-1 reverse transcriptase triphosphate binding site: Implications for nucleoside-analog drug resistance. Protein Science, 2000. 9(12): p. 2535-2546.

230.  Sigel H., C.P. Da Costa, B. Song, P. Carloni, and F. Gregan, Stability and structure of metal ion complexes formed in solution with acetyl phosphate and acetonylphosphonate: Quantification of isomeric equilibria. Journal of the American Chemical Society, 1999. 121(26): p. 6248-6257.

231.  Rovira C., P. Carloni, and M. Parrinello, The iron-sulfur bond in cytochrome c. Journal of Physical Chemistry B, 1999. 103(33): p. 7031-7035.

232.  Röthlisberger U. and P. Carloni, Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase. International Journal of Quantum Chemistry, 1999. 73(2): p. 209-218.

233.  Guidoni L., V. Torre, and P. Carloni, Potassium and sodium binding to the outer mouth of the K+ channel. Biochemistry, 1999. 38(27): p. 8599-8604.

234.  De Santis L. and P. Carloni, Serine proteases: An ab initio molecular dynamics study. Proteins-Structure Function and Genetics, 1999. 37(4): p. 611-618.

235.  Clementi C., P. Carloni, and A. Maritan, Protein design is a key factor for subunit-subunit association. Proceedings of the National Academy of Sciences of the United States of America, 1999. 96(17): p. 9616-9621.

236.  Alber F., G. Folkers, and P. Carloni, Dimethyl phosphate: Stereoelectronic versus environmental effects. Journal of Physical Chemistry B, 1999. 103(29): p. 6121-6126.

237.  Alber F., G. Folkers, and P. Carloni, Conformational analysis of dimethyl phosphate in aqueous solution: a density functional theory-based molecular dynamics study. Journal of Molecular Structure-Theochem, 1999. 489(2-3): p. 237-245.

238.  Carloni P. and F. Alber, Density-functional theory investigations of enzyme-substrate interactions. Perspectives in Drug Discovery and Design, 1998. 9-11: p. 169-179.

239.  Alber F., O. Kuonen, L. Scapozza, G. Folkers, and P. Carloni, Density functional studies on herpes simplex virus type 1 thymidine kinase-substrate interactions: The role of Tyr-172 and Met-128 in thymine fixation. Proteins-Structure Function and Bioinformatics, 1998. 31(4): p. 453-459.

240.  Carloni P., W. Andreoni, and M. Parrinello, Self-assembled peptide nanotubes from first principles. Physical Review Letters, 1997. 79(4): p. 761-764.

241.  Hutter J., P. Carloni, and M. Parrinello, Nonempirical calculations of a hydrated RNA duplex. Journal of the American Chemical Society, 1996. 118(36): p. 8710-8712.

242.  Carloni P. and W. Andreoni, Platinum-modified nucleobase pairs in the solid state: A theoretical study. Journal of Physical Chemistry, 1996. 100(45): p. 17797-17800.

243.  Banci L., P. Carloni, A. Diaz, and G.G. Savellini, Molecular dynamics calculations on peroxidases: The effect of calcium ions on protein structure. Journal of Biological Inorganic Chemistry, 1996. 1(3): p. 264-272.

244.  Tornaghi E., W. Andreoni, P. Carloni, J. Hutter, and M. Parrinello, Carboplatin Versus Cisplatin - Density-Functional Approach To Their Molecular-Properties. Chemical Physics Letters, 1995. 246(4-5): p. 469-474.

245.  Carloni P., P.E. Blochl, and M. Parrinello, Electronic-Structure Of The Cu, Zn Superoxide-Dismutase Active-Site And Its Interactions With The Substrate Journal of Physical Chemistry, 1995. 99(4): p. 1338-1348.

246.  Carloni P., P.E. Blochl, and P.L. Orioli, Electronic structure of crystalline (NH4)(2)CuCl4 from first principles. Gazzetta Chimica Italiana, 1995. 125(10): p. 497-500.

247.  Carloni P., W. Andreoni, J. Hutter, A. Curioni, P. Giannozzi, and M. Parrinello, Structure And Bonding In Cisplatin And Other Pt(II) Complexes. Chemical Physics Letters, 1995. 234(1-3): p. 50-56.

248.  Mangani S., P.L. Orioli, A. Scozzafava, L. Messori, and P. Carloni, EXAFS Studies Of Fe(III)-Phosvitin At High Metal To Protein Ratios. Biometals, 1994. 7(2): p. 104-108.

249.  Mangani S., P.L. Orioli, and P. Carloni, EXAFS Investigation On Nickel Substituted Cu, Zn Bovine Superoxide-Dismutase. Inorganica Chimica Acta, 1994. 216(1-2): p. 121-124.

250.  Banci L., P. Carloni, and G.G. Savellini, Molecular-Dynamics Studies On Peroxidases - A Structural Model For Horseradish-Peroxidase And A Substrate Adduct. Biochemistry, 1994. 33(41): p. 12356-12366.

251.  Banci L., P. Carloni, and P.L. Orioli, Molecular-Dynamics Studies On Mutants Of Cu, Zn Superoxide-Dismutase - The Functional-Role Of Charged Residues In The Electrostatic Loop-VII. Proteins-Structure Function and Genetics, 1994. 18(3): p. 216-230.

252.  Banci L., I. Bertini, B. Bruni, P. Carloni, C. Luchinat, S. Mangani, P.L. Orioli, M. Piccioli, W. Ripniewski, and K.S. Wilson, X-Ray, NMR And Molecular-Dynamics Studies On Reduced Bovine Superoxide-Dismutase - Implications For The Mechanism. Biochemical and Biophysical Research Communications, 1994. 202(2): p. 1088-1095.

253.  Banci L., I. Bertini, F. Capozzi, P. Carloni, S. Ciurli, C. Luchinat, and M. Piccioli, The Iron-Sulfur Cluster In The Oxidized High-Potential Iron Protein From Ectothiorhodospira-Halophila. Journal of the American Chemical Society, 1993. 115(9): p. 3431-3440.

254.  Mangani S., P. Carloni, M.S. Viezzoli, and J.E. Coleman, EXAFS Study Of The Active-Site Of Alkaline-Phosphatase From Escherichia-Coli. Inorganica Chimica Acta, 1992. 191(2): p. 161-165.

255.  Mangani S., P. Carloni, and P. Orioli, X-Ray-Diffraction Study Of The Interaction Between Carboxypeptidase-A And (S)-(+)-1-Amino-2-Phenylethyl Phosphonic Acid. European Journal of Biochemistry, 1992. 203(1-2): p. 173-177.

256.  Mangani S., P. Carloni, and P. Orioli, Crystal-Structure Of The Complex Between Carboxypeptidase-A And The Biproduct Analog Inhibitor L-Benzylsuccinate At 2.0-A Resolution. Journal of Molecular Biology, 1992. 223(2): p. 573-578.

257.  Mangani S., P. Carloni, and P. Orioli, X-Ray-Diffraction Studies On Carboxypeptidase-A Complexes - The Zinc Stereochemistry. Coordination Chemistry Reviews, 1992. 120: p. 309-324.

258.  Banci L., P. Carloni, G. Lapenna, and P.L. Orioli, Molecular-Dynamics Studies On Superoxide-Dismutase And Its Mutants - The Structural And Functional-Role Of ARG-143. Journal of the American Chemical Society, 1992. 114(18): p. 6994-7001.

259.  Banci L., I. Bertini, P. Carloni, C. Luchinat, and P.L. Orioli, Molecular-Dynamics Simulations On HIPIP From Chromatium-Vinosum And Comparison With NMR Data. Journal of the American Chemical Society, 1992. 114(27): p. 10683-10689.


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