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Self-Learning approaches
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
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* (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
Density biased sampling
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
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.
Path finding
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
Optimization and fine tuning
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
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