Replica Exchange
Publications in which techniques based on Replica Exchange Molecular Dynamics or related concepts were used/implemented
Publications in which techniques based on Replica Exchange Molecular Dynamics or related concepts were used/implemented
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MARINELLI F*, Faraldo-Gómez JD (2023). The molecular mechanism of selective and active transport in a Na+/Ca2+ exchanger. bioRxiv. 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
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
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
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
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