Publications

2021

  • 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. Cells 8 (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. Structure 27, 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 alConformational 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