Publications

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h-index: 24, citations: 4700 (Google Scholar, May 2025)

• Leone V, MARINELLI F* (2025). From snapshots to ensembles: Integrating experimental data and dynamics. Current Opinion in Structural Biology. Sep 15;95:103155. doi: 10.1016/j.sbi.2025.103155. Link 

• Tribello GA, Bonomi M, Bussi G, Camilloni C, Armstrong BI, Arsiccio A, Aureli S, Ballabio F, Bernetti M, Bonati L, Brookes SGH, Brotzakis ZF, Capelli R, Ceriotti M, Chan KT, Cossio P, Dasetty S, Donadio D, Ensing B, Ferguson AL, Fraux G, Gale JD, Gervasio FL, Giorgino T, Herringer NSM, Hocky GM, Hoff SE, Invernizzi M, Languin-Cattoën O, Leone V, Limongelli V, Lopez-Acevedo O, MARINELLI F, Febrer Martinez P, Masetti M, Mehdi S, Michaelides A, Murtada MH, Parrinello M, Piaggi PM, Pietropaolo A, Pietrucci F, Pipolo S, Pritchard C, Raiteri P, Raniolo S, Rapetti D, Rizzi V, Rydzewski J, Salvalaglio M, Schran C, Seal A, Shayesteh Zadeh A, Silva TFD, Spiwok V, Stirnemann G, Sucerquia D, Tiwary P, Valsson O, Vendruscolo M, Voth GA, White AD, Wu J. (2025) PLUMED Tutorials: A collaborative, community-driven learning ecosystem. J CHEM PHYS. 2025 Mar 07;162(9). Link

• Fiorin G, MARINELLI F, Forrest LR, Chen H, Chipot C, Kohlmeyer A, Santuz H, Henin J (2024). Expanded Functionality and Portability for the Colvars Library. J PHYS CHEM B ;128(45):11108-23. Epub 20241105. doi: 10.1021/acs.jpcb.4c05604. Link

• MARINELLI F*, Faraldo-Gómez JD (2024). Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity. PROC NATL ACAD SCI USA. 121: e2318009121. Link.

• Oh S, MARINELLI F#, Zhou, Lee J, Choi HJ, Kim M, Faraldo-Gómez JD, Hite RK (2022). Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+ channel TMEM175. eLIFE. 11: e75122. Link

• Lee PS, Bradshaw R, MARINELLI F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR (2021). Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software. LiveCoMS, vol. 3 (1), 1521. Link 

• MARINELLI F*, Faraldo-Gómez JD (2021). Force correction analysis method for derivation of multidimensional free energy landscapes from adaptively-biased replica simulations. J. Chem. Theory Comput. vol. 17; p. 6775–6788. Link

• Bradshaw RT,  MARINELLI F#,  Faraldo-Gómez JD ,  Forrest LR (2020). Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. BIOPHYS J. vol. 118; p. 1649-1664 . Link

• Fiorin G, MARINELLI F, Faraldo‐Gómez JD (2020). Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. J COMPUT CHEM vol 41; p. 449-459. Link 

• Bonomi M, Bussi G, Camilloni C, Tribello G, ..., MARINELLI F, et al. (2019) Promoting transparency and reproducibility in enhanced molecular simulations. NATURE METHODS vol. 16; p. 670–673. Link

• Li M, Wang Y, Banerjee R, MARINELLI F, Silberberg S, Faraldo-Gómez JD, Hattori M, Swartz KJ. Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP (2019). eLIFE 8:e47060. Link

• MARINELLI F*, Fiorin G (2019). Structural characterization of biomolecules through atomistic simulations guided by DEER measurements. STRUCTURE  vol. 27; p. 359-370. Link

• Hustedt EJ, MARINELLI F#, Stein RA, Faraldo-Gómez JD, Mchaourab HS (2018). Confidence Analysis of DEER Data and its Structural Interpretation with Ensemble-Biased Metadynamics. BIOPHYS J. vol. 115; p. 1200-1216. Link

• Shlosman I, MARINELLI F, Faraldo-Gómez JD, Mindell JA (2017). The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3:1 stoichiometry. J GEN PHYSIOL. doi: 10.1085/jgp.201711897. Link.

• Zhou W, MARINELLI F*, Nief C, Faraldo-Gómez JD (2017). Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore. eLIFE. doi: http://dx.doi.org/10.7554/eLife.23781. Link.

• Liao J, MARINELLI F#, Lee C, Huang Y, Faraldo-Gómez JD, Jiang Y (2016). Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger. NAT STRUCT MOL BIOL. doi:10.1038/nsmb.3230. Link.

• Branduardi D, MARINELLI F, Faraldo-Gómez JD (2015). Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method. J COMPUT CHEM vol. 37; p. 575-586. Link

• MARINELLI F*,  D, Faraldo-Gómez JD (2015). Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions. BIOPHYS J. vol. 108; p. 2779–2782. doi:10.1016/j.bpj.2015.05.024. Link

• MARINELLI F, Almagor L, Hiller R, Giladi M, Khananshvili D, Faraldo-Gómez JD (2014).  Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation. PROC NATL ACAD SCI USA. doi:10.1073/pnas.1415751111, PDF, Link

• MARINELLI F* (2013). Following Easy Slope Paths on a Free Energy Landscape: The Case Study of the Trp-Cage Folding Mechanism. BIOPHYS J, vol. 105; p. 1236–1247. ISSN: 0006-3495, PDF, Link 

• Carles Corbi-Verge, MARINELLI F#, Ana Zafra-Ruano, Javier Ruiz-Sanz, Irene Luque, and José D. Faraldo- Gómez (2013). Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap. PROC NATL ACAD SCI USA, vol. 110; p. E3372-E3380, ISSN: 1091-6490, PDF, Link

• Biarnes X, Pietrucci F, MARINELLI F, Laio A (2012). METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations. COMPUT PHYS COMMUN, vol. 183; p. 203-211, ISSN: 0010-4655, doi: 10.1016/j.cpc.2011.08.020, Link

• MARINELLI F*, Sorrenti A, Corvaglia V, Leone V, Mancini G (2012). Molecular description of the propagation of chirality from molecules to complex systems: different mechanisms controlled by hydrophobic interactions. CHEM-EUR J, vol. 18; p. 14680-14688, ISSN: 0947-6539, doi: 10.1002/chem.201202342, Link

• MARINELLI F, Kuhlmann SI, Grell E, Kunte HJ, Ziegler C, Faraldo-Gomez JD (2011). Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins. PROC NATL ACAD SCI USA, vol. 108; p. E1285-E1292, ISSN: 0027-8424, doi: 10.1073/pnas.1112534108, PDF, Link

• Cossio P, MARINELLI F, Laio A, Pietrucci F (2010). Optimizing the Performance of Bias-Exchange Metadynamics: Folding a 48-Residue LysM Domain Using a Coarse-Grained Model. J PHYS CHEM B, vol. 114; p. 3259-3265, ISSN: 1520-6106, doi: 10.1021/jp907464b, Link

• Leone V, MARINELLI F, Carloni P, Parrinello M (2010). Targeting biomolecular flexibility with metadynamics. CURR OPIN STRUCT BIOL, vol. 20; p. 148-154, ISSN: 0959-440X, doi: 10.1016/j.sbi.2010.01.011, Link

• Crespo Y, MARINELLI F*, Pietrucci F, Laio A (2010). Metadynamics convergence law in a multidimensional system. PHYS REV E, vol. 81, ISSN: 1539-3755, doi: 10.1103/PhysRevE.81.055701, Link

• Todorova N, MARINELLI F, Piana S, Yarovsky I (2009). Exploring the Folding Free Energy Landscape of Insulin Using Bias Exchange Metadynamics.J PHYS CHEM B, vol. 113; p. 3556-3564, ISSN: 1520-6106, doi: 10.1021/jp809776v, Link

• Pietrucci F, MARINELLI F, Carloni P, Laio A (2009). Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations. J AM CHEM SOC, vol. 131; p. 11811-11818, ISSN: 0002-7863, doi: 10.1021/ja903045y, Link

• Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, Donadio D, MARINELLI F, Pietrucci F, Broglia RA, Parrinello M (2009). PLUMED: A portable plugin for free-energy calculations with molecular dynamics. COMPUT PHYS COMMUN, vol. 180; p. 1961-1972, ISSN: 0010-4655, doi: 10.1016/j.cpc.2009.05.011, Link

• MARINELLI F, Pietrucci F, Laio A, Piana S (2009). A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations. PLOS COMPUT BIOL, vol. 5, ISSN: 1553-734X, doi: 10.1371/journal.pcbi.1000452, PDF, Link

• Piana S, Laio A, MARINELLI F, Van Troys M, Bourry D, Ampe C, Martins JC (2008). Predicting the effect of a point mutation on a protein fold: The villin and advillin headpieces and their Pro62Ala mutants. J MOL BIOL, vol. 375; p. 460-470, ISSN: 0022-2836, doi: 10.1016/j.jmb.2007.10.020, Link

• D'Abramo M, Aschi M, MARINELLI F, Di Nola A, Amadei A (2007). Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water. J MOL STRUC-THEOCHEM, vol. 811; p. 197-201, ISSN: 0166-1280, doi: 10.1016/j.theochem.2007.01.025, Link

• Amadei A, MARINELLI F, D'Abramo M, D'Alessandro M, Anselmi M, Di Nola A, Aschi M (2005). Theoretical modeling of vibroelectronic quantum states in complex molecular systems: Solvated carbon monoxide, a test case. J CHEM PHYS, vol. 122, ISSN: 0021-9606, doi: 10.1063/1.1870812, Link

• D'Alessandro M, MARINELLI F, D'Abramo M, Aschi M, Di Nola A, Amadei A (2005). Ground and excited electronic state thermodynamics of aqueous carbon monoxide: A theoretical study. J CHEM PHYS, vol. 122, ISSN: 0021-9606, doi: 10.1063/1.1870832, Link