Cignoni E., Lapillo M, Cupellini L, Acosta-Gutiérrez S, Gervasio F. L, Mennucci B. A different perspective for nonphotochemical quenching in plant antenna complexes. Nat. Commun.12, 7152 (2021). 10.1038/s41467-021-27526-8.
Galdadas I., Carlino L., Ward R. A., Hughes S. J., Haide S., Gervasio F. L. Structural Basis of the Effect of Activating Mutations on the EGF Receptor. eLife, 10, 1–24 (2021). 10.7554/eLife.65824.
Galdadas I., Qu, S., Oliveira A. S. F., Olehnovics E., Mack A. R., Mojica M. F., Agarwal P. K., Tooke C. L., Gervasio F. L., Spencer J., Bonomo R. A., Mulholland A. J., Haider S. Allosteric Communication in Class a β-Lactamases Occurs via Cooperative Coupling of Loop Dynamics. eLife, 10, 1–23 (2021). 10.7554/eLife.66567.
2020
Mattedi G., Acosta-Gutiérrez S, Clark T., Gervasio F.L., A combined activation mechanism for the glucagon receptor. Proc. Natl. Acad. Sci., 201921851 (2020). doi.org: 10.1073/pnas.1921851117.
Galdadas I., Gervasio F. L., Cournia Z. Unravelling the Effect of the E545K Mutation on PI3Kα Kinase. Chem. Sci. 2020, 16 (408supp), 6511–6512.(2020). doi.org: 10.1039/C9SC05903B.
Kuzmanic A., Bowman G. R., Juarez-Jimenez J., Michel J., Gervasio F. L. Investigating Cryptic Binding Sites by Molecular Dynamics Simulations. Acc. Chem. Res. (2020). doi: 10.1021/acs.accounts.9b00613.
2019
Estarellas C., Scaffidi S., Saladino G., Spyrakis F, Franzoni L., Galdeano C.,Bidon-ChanaAl, Gervasio F. L. and Luque F. L., J. Phys. Chem. Lett., 2019, 7333–7339. doi: 10.1021/acs.jpclett.9b02861
Yalinca H., Gehin C. J. C., Oleinikovas V., Lashuel H. A., Gervasio F. L., Pastore, A. The Role of Post-Translational Modifications on the Energy Landscape of Huntingtin N-Terminus. Front. Mol. Biosci.6, 1–7 (2019). doi: 10.3389/fmolb.2019.00095.
Martin-Fernandez M. L., Clarke D. T., Roberts S. K., Zanetti-Domingues L. C.& Gervasio F. L. Structure and Dynamics of the EGF Receptor as Revealed by Experiments and Simulations and Its Relevance to Non-Small Cell Lung Cancer. Cells8 (4), 316 (2019). doi: 10.3390/cells8040316.
Mattedi G., Deflorian F., Mason J. S., de Graaf C. & Gervasio F. L. Understanding Ligand Binding Selectivity in a Prototypical GPCR Family. J. Chem. Inf. Model. acs.jcim.9b00298 (2019). doi:10.1021/acs.jcim.9b00298.
Kuzmanic A., Pritchard R. B., Hansen D. F. & Gervasio, F. L. Importance of the Force-Field Choice in Capturing Functionally Relevant Dynamics in Von Willebrand Factor. J. Phys. Chem. Lett. acs.jpclett.9b00517 (2019). doi:10.1021/acs.jpclett.9b00517.
Yan R., Yalinca H., Paoletti F., Gobbo F., Marchetti, L. Kuzmanic, A. et al. The Structure of the Pro-domain of Mouse proNGF in Contact with the NGF Domain. Structure27, 78–89.e3 (2019). doi: 10.1016/j.str.2018.09.013.
Hovan L., Comitani F. & Gervasio, F. L. Defining an Optimal Metric for the Path Collective Variables. J. Chem. Theory Comput.15, 25–32 (2019). doi: 10.1021/acs.jctc.8b00563.
2018
S. Haldar, F. Comitani, G. Saladino, C. Woods, M. W. Van Der Kamp, A. J. Mulholland and F. L. Gervasio, J. Chem. Theory Comput., 14, 6093–6101 (2018). doi: 10.1021/acs.jctc.8b00687.
Zanetti-Domingues, L. C. et al. The architecture of EGFR’s basal complexes reveals autoinhibition mechanisms in dimers and oligomers. Nat. Commun.9, 4325 (2018). doi: 10.1038/s41467-018-06632-0.
Eelen, G. et al.Role of glutamine synthetase in angiogenesis beyond glutamine synthesis. Nature (2018). doi:10.1038/s41586-018-0466-7.
Galdadas, I., et al.Defining the architecture of KPC-2 Carbapenemase: identifying allosteric networks to fight antibiotics resistance. Sci. Rep. 8, 12916.(2018). doi:10.1038/s41598-018-31176-0
Comitani, F., & Gervasio, F. L. Exploring Cryptic Pockets Formation in Targets of Pharmaceutical Interest with SWISH. J. Chem. Theory Comput. (2018). doi:10.1021/acs.jctc.8b00263
Ordan, M., et al. Intrinsically active MEK variants are differentially regulated by proteinases and phosphatases. Sci. Rep. 8 (1), 11830. (2018). doi:10.1038/s41598-018-30202-5
Tsuchiya, Y., et al.Protein CoAlation and antioxidant function of Coenzyme A in prokaryotic cells. Biochem. J. (2018). doi:10.1042/bcj20180043
2017
Saleh, N., Ibrahim, P., Saladino, G., Gervasio, F. L., & Clark, T. An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. J. Chem. Inf. Model. (2017). doi:10.1021/acs.jcim.6b00772
Hovan, L., Oleinikovas, V., Yalinca, H., Kryshtafovych, A., Saladino, G., & Gervasio, F. L. Assessment of the model refinement category in CASP12. Proteins. (2017). doi:10.1002/prot.25409
Kuzmanic, A., Sutto, L., Saladino, G., Nebreda, A. R., Gervasio, F. L., & Orozco, M. Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations. eLife, 6. (2017). doi:10.7554/eLife.22175
Perdios, P., et al. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET.Sci. Rep. (2017). doi:10.1038/srep39841
Saleh, N., Saladino, G., Gervasio, F. L., & Clark, T. Investigating allosteric effects on the functional dynamics of [small beta]2-adrenergic ternary complexes with enhanced-sampling simulations. Chem. Sci., 8 (5), 4019-4026. (2017). doi:10.1039/C6SC04647A
Ruiz-Perez, L., Messager, L., Gaitzsch, J., Joseph, A., Sutto, L., Gervasio, F. L., & Battaglia, G. (2017). Polymersome membrane-confined self-assembly. Presented at: 253rd National Meeting of the American-Chemical-Society (ACS) on Advanced Materials, Technologies, Systems, and Processes.
Saladino, G., Estarellas, C., & Gervasio, F. L. (2017). Recent Progress in Free Energy Methods. Comprehensive Medicinal Chemistry III (pp. 34-50). doi:10.1016/B978-0-12-409547-2.12356-X
2016
Saleh, N., et al. A Three-Site Mechanism for Agonist/Antagonist Selective Binding to Vasopressin Receptors.Angew. Chem. Int. Ed. Engl., 55 (28), 8008-8012. (2016). doi:10.1002/anie.201602729
Ruiz-Pérez, L., Messager, L., Gaitzsch, J., Joseph, A., Sutto, L., Gervasio, F. L., & Battaglia, G. Molecular engineering of polymersome surface topology. Sci. Adv., 2 (4), e1500948. (2016). doi:10.1126/sciadv.1500948
Papaleo, E., Saladino, G., Lambrughi, M., Lindorff-Larsen, K., Gervasio, F. L., & Nussinov, R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem. Rev., 116 (11), 6391-6423. (2016). doi:10.1021/acs.chemrev.5b00623
Oleinikovas, V., Saladino, G., Cossins, B. P., & Gervasio, F. L. Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations. J. Am. Chem. Soc., 138 (43), 14257-14263. (2016). doi:10.1021/jacs.6b0542
Pucheta-Martinez, et al. An Allosteric Cross-Talk Between the Activation Loop and the ATP Binding Site Regulates the Activation of Src Kinase. Sci. Rep., 6, ARTN 24235. (2016). doi:10.1038/srep24235
Schulze, J. O., et al. Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase. Cell Chem Biol. (2016). doi:10.1016/j.chembiol.2016.06.017
Pucheta-Martinez, E., D’Amelio, N., Lelli, M., Martinez-Torrecuadrada, J. L., Sudol, M., Saladino, G., & Gervasio, F. L. Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome. Sci. Rep., 6, ARTN 30293. (2016). doi:10.1038/srep30293
Agnese Morando, et al. Conformational Selection and Induced Fit Mechanisms in the Binding of an Anticancer Drug to the c-Src Kinase.Sci. Rep., 6, ARTN 24439. (2016). doi:10.1038/srep24439
Lambrughi, M., et al. DNA-binding protects p53 from interactions with cofactors involved in transcription-independent functions.Nucleic Acids Res., gkw770. (2016). doi:10.1093/nar/gkw770
Saladino, G., & Gervasio, F. L. Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases. Curr. Opin. Struct. Biol., 37, 108-114.(2016). doi:10.1016/j.sbi.2016.01.005
Herbert, C., et al. Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling. Cancer Cell, 30 (1), 176-178.(2016). doi:10.1016/j.ccell.2016.06.015
2015
Sutto, L., Marsili, S., Valencia, A., & Gervasio, F. L. From residue coevolution to protein conformational ensembles and functional dynamics. Proc. Natl. Acad. Sci. U.S.A., 112 (44), 13567-13572.(2015). doi:10.1073/pnas.1508584112
Cavalli, A., Spitaleri, A., Saladino, G., & Gervasio, F. L. Investigating Drug–Target Association and Dissociation Mechanisms Using Metadynamics-Based Algorithms. Acc. Chem. Res., 48 (2), 277-285. (2015). doi:10.1021/ar500356n
Marino, K. A., Sutto, L., & Gervasio, F. L. The Effect of a Widespread Cancer-Causing Mutation on the Inactive to Active Dynamics of the B-Raf Kinase. J. Am. Chem. Soc., 137, 5280-5283. (2015). doi:10.1021/jacs.5b01421
Doro, F., Saladino, G., Belvisi, L., Civera, M., & Gervasio, F. L. New Insights into the Molecular Mechanism of E-Cadherin-Mediated Cell Adhesion by Free Energy Calculations. J. Chem. Theory Comp., 11, 1354-1359. (2015). doi:10.1021/ct5010164
Bunney, T. D., et al. The Effect of Mutations on Drug Sensitivity and Kinase Activity of Fibroblast Growth Factor Receptors: A Combined Experimental and Theoretical Study. EBioMedicine, 2 (3), 194-204. (2015). doi:10.1016/j.ebiom.2015.02.009
Lovera, S., et al. Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics. Plos Comp. Biol., 11 (11), ARTN e1004578. (2015). doi:10.1371/journal.pcbi.1004578
2014
Papaleo, E., Sutto, L., Gervasio, F. L., & Lindorff-Larsen, K. Conformational Changes and Free Energies in a Proline Isomerase. J. Chem. Theory Comp., 10, 4169-4174. (2014). doi:10.1021/ct500536r
Wolkenhauer, O. et al.Enabling multiscale modeling in systems medicine.Genome Med.6, 4–6. (2014). doi:10.1186/gm538
Dölker, N., Górna, M. W., Sutto, L., Torralba, A. S., Superti-Furga, G., & Gervasio, F. L. The SH2 Domain Regulates c-Abl Kinase Activation by a Cyclin-Like Mechanism and Remodulation of the Hinge Motion.Plos Comp. Biol. (2014). doi: 10, e1003863
Goñi, G. M., et al. Phosphatidylinositol 4,5-bisphosphate triggers activation of focal adhesion kinase by inducing clustering and conformational changes. Proc. Natl. Acad. Sci. U.S.A., 111, E3177-E3186. (2014). doi:10.1073/pnas.1317022111
2013
Sutto, L., & Gervasio, F. L. Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase. Proc. Natl. Acad. Sci. U.S.A., 110 (26), 10616-10621. (2013). doi:10.1073/pnas.1221953110
Juraszek, J., Saladino, G., van Erp, T. S., & Gervasio, F. L. Efficient Numerical Reconstruction of Protein Folding Kinetics with Partial Path Sampling and Pathlike Variables. Phys. Rev. Lett., 110, 108106. (2013). doi:10.1103/PhysRevLett.110.108106
Herbert, C., et al. Molecular Mechanism of SSR128129E, an Extracellularly Acting, Small-Molecule, Allosteric Inhibitor of FGF Receptor Signaling. Cancer Cell, 23, 489-501. (2013). doi: 10.1016/j.ccr.2013.02.018
Sahún-Roncero, M., et al. The mechanism of allosteric coupling in choline kinase α1 revealed by the action of a rationally designed inhibitor. Angew. Chem. Int. Ed. Engl., 52 (17), 4582-4586. (2013). doi:10.1002/anie.201209660
Bono, F. C. C., et al. Inhibition of Tumor Angiogenesis and Growth by a Small-Molecule Multi-FGF Receptor Blocker with Allosteric Properties. Cancer Cell, 23, 477-488. doi: 10.1016/j.ccr.2013.02.019
Saladino, G., Gauthier, L., Bianciotto, M., & Gervasio, F. L. Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors. J. Chem. Theory Comp., 8 (4), 1165-1170. (2012). doi:10.1021/ct3001377
2012
Sutto, L., Marsili, S., & Gervasio, F. L. (2012). New advances in metadynamics. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2 (5), 771-779. doi:10.1002/wcms.1103
D’Abramo, M., Rabal, O., Oyarzabal, J., & Gervasio, F. L. Conformational Selection versus Induced Fit in Kinases: The Case of PI3K-gamma. Angew. Chem. Int. Ed. Engl., 51 (3), 642-646. (2012). doi:10.1002/anie.201103264
Lovera, S., Sutto, L., Boubeva, R., Scapozza, L., Doelker, N., & Gervasio, F. L. The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation. J. Am. Chem. Soc. 134 (5), 2496-2499. (2012). doi:10.1021/ja210751t
Saladino, G., & Gervasio, F. L. New insights in protein kinase conformational dynamics. Curr. Top. Med. Chem., 12 (17), 1889-1895. (2012). doi:10.2174/1568026611209061889
Molina, R., et al. Non-specific protein-DNA interactions control I-CreI target binding and cleavage. Nucleic Acids Res., 40 (14), 6936-6945. (2012). doi:10.1093/nar/gks320
Besker, N., & Gervasio, F. L. (2012). Using Metadynamics and Path Collective Variables to Study Ligand Binding and Induced Conformational Transitions. In R. Baron (Ed.), Computational Drug Discovery and Design (pp. 501-513). doi:10.1007/978-1-61779-465-0_29
Sutto, L., Mereu, I., & Luigi Gervasio, F. A Hybrid All-Atom Structure-Based Model for Protein Folding and Large Scale Conformational Transitions. J. Chem. Theory Comp., 7 (12), 4208-4217. (2011). doi:10.1021/ct200547m
2011
Saladino, G., Marenchino, M., Pieraccini, S., Campos-Olivas, R., Sironi, M., & Gervasio, F. L. A Simple Mechanism Underlying the Effect of Protecting Osmolytes on Protein Folding. J. Chem. Theory Comp., 7 (11), 3846-3852. (2011). doi:10.1021/ct200471w
Campos-Olivas, R., Marenchino, M., Scapozza, L., & Gervasio, F. L. Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib. Biomolecular Nmr Assignments, 5 (2), 221-224. (2011). doi:10.1007/s12104-011-9304-7
Campos-Olivas, R., Marenchino, M., Gervasio, F. L., & Scapozza, L. Backbone assignment of the tyrosine kinase Src catalytic domain in complex with imatinib. Biomolecular NMR Assignments, 1-4. (2011). doi:10.1007/s12104-011-9304-7
Saladino, G., Marenchino, M., & Gervasio, F. L. Bridging the Gap between Folding Simulations and Experiments: The Case of the Villin Headpiece. J. Chem. Theory Comp., 7 (9), 2675-2680. (2011). doi:10.1021/ct2002489
Sutto, L., Mereu, I., & Gervasio, F. L. Characterizeing the activation of protein kinase through an hybrid all-atom structure-based model. Eur. Biophys. J., 40, 118. (2011).
De Vivo, M., Bottegoni, G., Berteotti, A., Recanatini, M., Luigi Gervasio, F., & Cavalli, A. (2011). Cyclin-dependent kinases: bridging their structure and function through computations. Future Medicinal Chemistry, 3 (12), 1551-1559. doi:10.4155/fmc.11.113
Munoz, I. G., et al. Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus. Nucleic Acids Res., 39 (2), 729-743. (2011). doi:10.1093/nar/gkq801
Boubeva, R., Cristiani, A., Pernot, L., Perozzo, R., Sutto, L., Scapozza, L., & Gervasio, F. L. (2011). Understanding the plasticity of c-Src tyrosine kinase through very long molecular dynamics simulations and experimentally validated free energy calculations. Eur. Biophys. J., 40, 207-208.
2010
Limongelli, V., Bonomi, M., Marinelli, L., Luigi Gervasio, F., Cavalli, A., Novellino, E., & Parrinello, M. (2010). Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proc. Natl. Acad. Sci. U.S.A., 107 (12), 5411-5416. (2010). doi:10.1073/pnas.0913377107
Sutto, L., D’Abramo, M., & Luigi Gervasio, F. Comparing the Efficiency of Biased and Unbiased Molecular Dynamics in Reconstructing the Free Energy Landscape of Met-Enkephalin. J. Chem. Theory Comp., 6 (12), 3640-3646. (2010). doi:10.1021/ct100413b
Fidelak, J., Juraszek, J., Branduardi, D., Bianciotto, M., & Luigi Gervasio, F. Free-Energy-Based Methods for Binding Profile Determination in a Congeneric Series of CDK2 Inhibitors. J. Phys. Chem. B, 114 (29), 9516-9524. (2012). doi:10.1021/jp911689r
Bonomi, M., Barducci, A., Gervasio, F. L., & Parrinello, M. Multiple Routes and Milestones in the Folding of HIV-1 Protease Monomer. Plos One, 5 (10). (2010). doi:10.1371/journal.pone.0013208
2009
Cucinotta, C. S., Kosa, M., Melchiorre, P., Cavalli, A., & Gervasio, F. L. Bifunctional Catalysis by Natural Cinchona Alkaloids: A Mechanism Explained. Chemistry-a Eur. J., 15 (32), 7913-7921. (2009). doi:10.1002/chem.200900406
Masetti, M., Cavalli, A., Recanatini, M., & Gervasio, F. L. Exploring Complex Protein-Ligand Recognition Mechanisms with Coarse Metadynamics. J. Phys. Chem. B, 113 (14), 4807-4816. (2009). doi:10.1021/jp803936q
Berteotti, A., Cavalli, A., Branduardi, D., Gervasio, F. L., Recanatini, M., & Parrinello, M. Protein Conformational Transitions: The Closure Mechanism of a Kinase Explored by Atomistic Simulations. J. Am. Chem. Soc., 131 (1), 244-250. (2009). doi:10.1021/ja806846q
2008
Domene, C., Klein, M. L., Branduardi, D., Gervasio, F. L., & Parrinello, M. Conformational changes and gating at the selectivity filter of potassium channels. J. Am. Chem. Soc., 130 (29), 9474-9480. (2008). doi:10.1021/ja801792g
Laio, A., & Gervasio, F. L. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys., 71 (12). (2008). doi:10.1088/0034-4885/71/12/126601
Petraglio, G., et al. The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge. Proteins, 70 (3), 779-785. (2008). doi:10.1002/prot.21560
Bonomi, M., Branduardi, D., Gervasio, F. L., & Parrinello, M. The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin. J. Am. Chem. Soc., 130 (42), 13938-13944. (2008). doi:10.1021/ja803652f
2007
Bonomi, M., Branduardi, D., Gervasio, F. L., & Parrinello, M. The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin.J. Am. Chem. Soc., 130 (42), 13938-13944. (2007). doi:10.1021/ja803652f
Boero, M., Gervasio, F. L., & Parrinello, M. Charge localisation and hopping in DNA. Molecular Sim., 33 (1-2), 57-60. (2007). doi:10.1080/08927020601052849
Mantz, Y. A., Luigi Gervasio, F., Laino, T., & Parrinello, M. Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory. J. Phys. Chem. A, 111 (1), 105-112. (2007). doi:10.1021/jp063080n
Gervasio, F. L. Charge transfer mechanism in a PolydGpdCp fiber and in wet DNA. Comp. Phys. Commun., 177 (1-2), 27-29. (2007) doi:10.1016/j.cpc.2007.02.109
Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M. (2007). COMP 463-Free-energy landscapes from combined parallel-tempering and metadynamics. Abstracts of Papers of the American Chemical Society, 234.
Branduardi, D., Gervasio, F. L., & Parrinello, M. From A to B in free energy space. J. Chem. Phys., 126 (5). (2007) doi:10.1063/1.2432340
Bonomi, M., Gervasio, F. L., Tiana, G., Provasi, D., Broglia, R. A., & Parrinello, M. Insight into the folding inhibition of the HIV-1 protease by a small peptide. Biophys. J., 93 (8), 2813-2821. (2007). doi:10.1529/biophysj.107.106369
Dal Peraro, M., Ruggerone, P., Raugei, S., Gervasio, F. L., & Carloni, P. Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations. Curr. Opin. Struct. Biol., 17 (2), 149-156. doi:10.1016/j.sbi.2007.03.018
Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M. PHYS 410-Beta-hairpin folding with parallel-tempering and metadynamics. Abstracts of Papers of the American Chemical Society, 234.
Mantz, Y. A., Gervasio, F. L., Laino, T., & Parrinello, M. (2007). PHYS 546-Hydration effects on charge spatial extent in DNA and implications for transfer: A theoretical SIC-QM/MM study. Abstracts of Papers of the American Chemical Society, 234.
Cavalli, A., Berteotti, A., Branduardi, D., Gervasio, F. L., Recanatini, M., & Parrinello, M. (2007). Protein conformational plasticity: the “off-on” switching movement in Cdk5. In T. E. Simos, G. Maroulis (Eds.), Computation in Modern Science and Engineering Vol 2, Pts a and B (p. 598).
Mantz, Y. A., Gervasio, F. L., Laino, T., & Parrinello, M. Solvent effects on charge spatial extent in DNA and implications for transfer. Phys. Rev. Lett., 99 (5). (2007). doi:10.1103/PhysRevLett.99.058104
2006
Raugei, S., Gervasio, F. L., & Carloni, P. DFT modeling of biological systems. Phys. Status Solidi B, 243 (11), 2500-2515. (2006). doi:10.1002/pssb.200642096
Gervasio, F. L., Boero, M., & Parrinello, M. Double proton coupled charge transfer in DNA. Angew. Chem. Int. Ed., 45 (34), 5606-5609. (2006). doi:10.1002/anie.200602106
Raiteri, P., Laio, A., Gervasio, F. L., Micheletti, C., & Parrinello, M. Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. J. Phys. Chem. B, 110 (8), 3533-3539. (2006). doi:10.1021/jp054359r
Gervasio, F. L., Parrinello, M., Ceccarelli, M., & Klein, M. L. Exploring the gating mechanism in the ClC chloride channel via metadynamics. J.Mol. Biol., 361 (2), 390-398. (2006). doi:10.1016/j.jmb.2006.06.034
Bussi, G., Gervasio, F. L., Laio, A., & Parrinello, M. Free energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J. Am. Chem. Soc., 128 (41), 13435-13441. (2006). doi:10.1021/ja062463w
Barducci, A., Chelli, R., Procacci, P., Schettino, V., Gervasio, F. L., & Parrinello, M. Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding. J. Am. Chem. Soc., 128 (8), 2705-2710. (2006). doi:10.1021/ja057076l
2005
Laio, A., Rodriguez-Fortea, A., Gervasio, F. L., Ceccarelli, M., & Parrinello, M. Assessing the accuracy of metadynamics. J.Phys. Chem. B, 109 (14), 6714-6721. (2005). doi:10.1021/jp045424k
Gervasio, F. L., Laio, A., Parrinello, M., & Boero, M. Charge localization in DNA fibers. Phys. Rev. Lett., 94 (15). (2005). doi:10.1103/PhysRevLett.94.158103
Gervasio, F. L., Laio, A., & Parrinello, M. Flexible docking in solution using metadynamics. J. Am. Chem. Soc., 127 (8), 2600-2607. (2005). doi:10.1021/ja0445950
Gervasio, F. L. (2005). Performance of metadynamics in flexible docking. Abstracts of Papers of the American Chemical Society, 229, U766.
Branduardi, D., Gervasio, F. L., Cavalli, A., Recanatini, M., & Parrinello, M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. J. Am. Chem. Soc., 127 (25), 9147-9155. (2005). doi:10.1021/ja0512080
Gervasio, F. L., Laio, A., & Parrinello, M. (2005). Translocation mechanism of ions in channels and enzymatic gorges. Abstracts of Papers of the American Chemical Society, 230, U2958.
2004
Ensing, B., Laio, A., Gervasio, F. L., Parrinello, M., & Klein, M. L. A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion. J. Am. Chem. Soc., 126 (31), 9492-9493. (2004). doi:10.1021/ja048285t
Laio, A., Gervasio, F. L., VandeVondele, J., Sulpizi, M., & Rothlisberger, U. A variational definition of electrostatic potential derived charges. J. Phys. Chem. B, 108 (23), 7963-7968. (2004). doi:10.1021/jp0496405
Gervasio, F. L., Laio, A., Iannuzzi, M., & Parrinello, M. Influence of DNA structure on the reactivity of the guanine radical cation. Chemistry-a European Journal, 10 (19), 4846-4852. (2004). doi:10.1002/chem.200400171
Chelli, R., Gervasio, F. L., Procacci, P., & Schettino, V. Inter-residue and solvent-residue interactions in proteins: A statistical study on experimental structures. Proteins, 55 (1), 139-151. (2004). doi:10.1002/prot.20030
Gervasio, F. L., & Parrinello, M. (2004). Mechanism of DNA oxidation. Abstracts of Papers of the American Chemical Society, 227, U1001.
2003
Ensing, B., Gervasio, F. L., Laio, A., Parrinello, M., & Klein, M. L. (2003). Ab initio molecular dynamics study of the E2 and Sn2 reaction between X-+CH3CH2Y. Abstracts of Papers of the American Chemical Society, 226, U303.
Gervasio, F. L., Schettino, V., Mangani, S., Krack, M., Carloni, P., & Parrinello, M. Influence of outer-shell metal ligands on the structural and electronic properties of horse liver alcohol dehydrogenase zinc active site. J. Phys. Chem. B, 107 (28), 6886-6892. (2003). doi:10.1021/jp027567h
Gervasio, F. L., Laio, A., Iannuzzi, M., & Parrinello, M. (2003). Mechanism of oxidative damage to DNA. Eur. Biophys. J., 32 (3), 208.
2002
Gervasio, F. L., Carloni, P., & Parrinello, M. Electronic structure of wet DNA. Phys. Rev. Lett., 89 (10). (2002). doi:10.1103/PhysRevLett.89.108102
Gervasio, F. L., Chelli, R., Procacci, P., & Schettino, V. Is the T-shaped toluene dimer a stable intermolecular complex?. J. Phys.Chem. A, 106 (12), 2945-2948. (2002). doi:10.1021/jp0137975
Chelli, R., Gervasio, F. L., Procacci, P., & Schettino, V. Stacking and T-shape competition in aromatic-aromatic amino acid interactions. J. Ame. Chem. Soc., 124 (21), 6133-6143. (2002). doi:10.1021/ja0121639
Gervasio, F. L., Chelli, R., Procacci, P., & Schettino, V. The nature of intermolecular interactions between aromatic amino acid residues. Proteins, 48 (1), 117-125. (2002). doi:10.1002/prot.10116
2001
Gervasio, F. L., Chelli, R., Marchi, M., Procacci, P., & Schettino, V. Determination of the potential of mean force of aromatic amino acid complexes in various solvents using molecular dynamics simulations: The case of the tryptophan-histidine pair. J. Phys. Chem. B, 105 (32), 7835-7846. (2001). doi:10.1021/jp010434w
Gervasio, F. L., Schettino, V., Mangani, S., Carloni, P., & Parrinello, M. Supraligand fine tuning of Zn-based enzymes: the case of Horse Liver alcohol dehydrogenase. J. Inorg.c Biochem., 86 (1), 233. (2001).
2000
Chelli, R., Gervasio, F. L., Gellini, C., Procacci, P., Cardini, G., & Schettino, V. Conformational distribution of gas-phase glycerol. J. Phys. Chem. A, 104 (47), 11220-11222. (2000). doi:10.1021/jp002677e
Gervasio, F. L., Procacci, P., Cardini, G., Guarna, A., Giolitti, A., & Schettino, V. Interaction between aromatic residues. Molecular dynamics and ab initio exploration of the potential energy surface of the tryptophan-histidine pair. J. Phys. Chem. B, 104 (5), 1108-1114. (2000). doi:10.1021/jp992208g
1999
Schettino, V., Gervasio, F. L., Cardini, G., & Salvi, P. R. Density functional calculation of structure and vibrational spectra of polyenes. J. Chem. Phys., 110 (6), 3241-3250. (1999). doi:10.1063/1.477847
Schettino, V., Gervasio, F. L., Cardini, G., & Salvi, P. R. (1999). Density functional calculation of the vibrational spectra of linear polyenes. Abstracts of Papers of the American Chemical Society, 217, U322.
1998
Gervasio, F. L., Cardini, G., Salvi, P. R., & Schettino, V. Low-frequency vibrations of all-trans-retinal: Far-infrared and Raman spectra and density functional calculations. J. Phys. Chem. A, 102 (12), 2131-2136. (1998). doi:10.1021/jp9724636