Publications

****2024

  • A Borsatto, E Gianquinto, V Rizzi, FL Gervasio SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein–Protein Interfaces J Chem Theor Comp. 2024, 20, 3335-3348 (https://doi.org/10.1021/acs.jctc.3c01318)

  • JC Calderón, E Plut, M Keller, C Cabrele, O Reiser, FL Gervasio, T Clark Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors J. Chem. Inf. and Model. 2023, 64, 205-218 (https://doi.org/10.1021/acs.jcim.3c01574)

  • Iyer, R. S., Needham, S. R., Galdadas, I., Davis, B. M., Roberts, S. K. Man, R. C. H., Zanetti-Domingues, L. C., Clarke, D. T., Fruhwirth, G. O., Parker, P. J., Rolfe, D. J., Gervasio F. L.* & Martin-Fernandez M. L. Nature Communications 2024, 15, 2130

****2023

  • Juyoux, P; Galdadas, I; Gobbo, D; Von Velsen, J; Pelosse, M.; Tully, M; Vadas, O; Gervasio, F.L.; Pellegrini, E; Bowler, M.W. Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation. Science, 2023, 381, 1217-1225. doi.org: 10.1126/science.add7859
  • C Qi, S Acosta-Gutierrez, P Lavriha, A Othman, D Lopez-Pigozzi, E Bayraktar, D Schuster, P Picotti, N Zamboni, M Bortolozzi, F. L. Gervasio*, Volodymyr M. Korkhov* Structure of the connexin-43 gap junction channel in a putative closed state eLife 2023,12:RP87616. (DOI: https://doi.org/10.7554/eLife.87616)
  • Radoux-Mergault, A.; Oberhauser, L.; Aureli, S.; Gervasio, F. L.; Stoeber, M. Subcellular location defines GPCR signal transduction. Sci. Adv., 2023, 9 (16), eadf6059. doi.org: 10.1126/sciadv.adf6059
  • Calderón, J. C.; Ibrahim, P.; Gobbo, D.; Gervasio, F. L.; Clark, T. General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. J. Chem. Inf. Model., 2023. doi.org: 10.1021/acs.jcim.3c00208
  • Rizzi, V.; Aureli, S.; Ansari, N.; Gervasio, F. L. OneOPES, a combined enhanced sampling method to rule them all. bioRxiv, 2023. doi.org: 10.1101/2023.03.06.531337
  • Karrenbrock, M.; Procacci, P.; Gervasio, F. L. A nonequilibrium alchemical method for drug-receptor absolute binding free energy calculations: the role of restraints. ChemRxiv, 2023. doi.org: 10.26434/chemrxiv-2023-mc1gw

2022

  • Haldar, S.; Zhang, Y.; Xia, Y.; Islam, B.; Liu, S.; Gervasio, F. L.; Mulholland, A. J.; Waller, Z. A. E.; Wei, D.; Haider, S. Mechanistic Insights into the Ligand-Induced Unfolding of an RNA G-Quadruplex. J. Am. Chem. Soc., 2022, 144 (2), 935–950. doi.org: 10.1021/jacs.1c11248
  • Di Gaetano, S.; Pirone, L.; Galdadas, I.; Traboni, S.; Iadonisi, A.; Pedone, E.; Saviano, M.; Gervasio, F. L.; Capasso, D. Design, Synthesis, and Anticancer Activity of a Selenium-Containing Galectin-3 and Galectin-9N Inhibitor. Int. J. Mol. Sci., 2022, 23 (5), 2581. doi.org: 10.3390/ijms23052581
  • Lukauskis, D.; Samways, M. L.; Aureli, S.; Cossins, B. P.; Taylor, R. D.; Gervasio, F. L. Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses. J. Chem. Inf. Model., 2022, 62 (23), 6209–6216. doi.org: 10.1021/acs.jcim.2c01142
  • Borsatto, A.; Akkad, O.; Galdadas, I.; Ma, S.; Damfo, S.; Haider, S.; Kozielski, F.; Estarellas, C.; Gervasio, F. L. Revealing Druggable Cryptic Pockets in the Nsp1 of SARS-CoV-2 and Other β-Coronaviruses by Simulations and Crystallography. eLife, 2022, 11. doi.org: 10.7554/eLife.81167

2021

  • 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 2021, 10, 1–23. doi.org: 10.7554/eLife.66567.
  • Galdadas, I.; Carlino, L.; Ward, R. A.; Hughes, S. J.; Shozeb, H.; Gervasio, F. L. Structural Basis of the Effect of Activating Mutations on the EGF Receptor. eLife, 2021, 10, doi.org: DOI:10.7554/eLife.65824
  • Ilmjärv, S.; Abdul, F.; Acosta-Gutiérrez, S.; Estarellas, C.; Galdadas, I.; Casimir, M.; Alessandrini, M.; Gervasio, F. L.; Krause, K.-H. Concurrent Mutations in RNA-dependent RNA Polymerase and Spike Protein Emerged as the Epidemiologically Most Successful SARS-CoV-2 Variant. Sci. Rep., 2021, 11 (1), 1–13. doi.org: [link]
  • Jesus, C. N.; Evans, R.; Forth, J.; Estarellas, C.; Gervasio, F. L.; Battaglia, G. Amphiphilic Histidine-Based Oligopeptides Exhibit pH-Reversible Fibril Formation. ACS Macro Lett., 2021, 10 (8), 984–989. doi.org: 10.1021/acsmacrolett.1c00142
  • Galdadas, I.; Carlino, L.; Ward, R. A.; Hughes, S. J.; Haider, S.; Gervasio, F. L. Structural Basis of the Effect of Activating Mutations on the EGF Receptor. Elife, 2021, 10, e65824. doi.org: 10.7554/eLife.65824
  • Ing, G.; De Pace, C.; Acosta Guitierrez, S.; Marchello, G.; Pilotto, S.; Leite, D.; Wilkinson, N.; Gervasio, F. L.; Werner, F.; Ruiz-Perez, L.; Battaglia, G. Liquid-Phase Electron Microscopy in Structural Protein Studies. Microsc. Microanal., 2021, 27 (S2), 89–90. doi.org: 10.1017/S1431927621013441
  • De Pace, C.; Acosta-Gutierrez, S.; Ing, G.; Marchello, G.; Pilotto, S.; Werner, F.; Wilkinson, N.; Leite, D.; Gervasio, F. L.; Ruiz-Pérez, L.; Battaglia, G. Imaging Protein Dynamics in Liquid Water. Microsc. Microanal., 2021, 27 (S2), 15–16. doi.org: 10.1017/S1431927621013076
  • 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., 2021, 12 (1), 7152. doi.org: 10.1038/s41467-021-27526-8

2020

  • Evans, R.; Hovan, L.; Tribello, G. A.; Cossins, B. P.; Estarellas, C.; Gervasio, F. L. Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies. J. Chem. Theory Comput, 2020, 16 (7), 4641–4654. doi.org: 10.1021/acs.jctc.0c00075.
  • G. Mattedi, S. Acosta-Gutiérrez, T. Clark, F. L. Gervasio, 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

  • C. Estarellas, S. Scaffidi, G. Saladino, F. Spyrakis, L. Franzoni, C. Galdeano, A. Bidon-Chanal, F. L. Gervasio and F. J. Luque, 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 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