Medical College of Wisconsin
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Fabrizio Marinelli PhD

Fabrizio Marinelli PhD profile photo picture

Associate Professor

Institution: Medical College of Wisconsin
Department: Biophysics
Program: Research

Member of the Cancer Center
Member of the Data Science Institute


I am willing to collaborate on research projects.
I am willing to be a peer mentor.

View Curriculum Vitae

Research Areas of Interest

  • Artificial Intelligence
  • Computational Biology
  • Electron Spin Resonance Spectroscopy
  • Machine Learning
  • Membrane Transport Proteins
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Proteins

    • Research Experience

  • Cell Membrane
  • Computer Simulation
  • Electron Spin Resonance Spectroscopy
  • Machine Learning
  • Membrane Transport Proteins
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Protein Folding
  • Quantum Theory

    • Methodologies and Techniques

  • Computer Simulation
  • Ion Channels
  • Membrane Transport Proteins
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Protein Conformation

    • Leadership Positions

  • Recruitment Director of the Biophysics graduate program

    • Educational Expertise

  • Cell Membrane
  • Computer Simulation
  • Machine Learning
  • Membrane Transport Proteins

    • Publications (36)

  • From snapshots to ensembles: Integrating experimental data and dynamics (Leone V, Marinelli F) Current Opinion in Structural Biology December 2025;95 SCOPUS ID: 2-s2.0-105015421270 12/01/2025       1 Citation
  • PLUMED Tutorials: A collaborative, community-driven learning ecosystem. (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) J Chem Phys 2025 Mar 07;162(9) PMID: 40035582 PMCID: PMC12317779 SCOPUS ID: 2-s2.0-86000483661 03/04/2025       8 Citations
  • Expanded Functionality and Portability for the Colvars Library. (Fiorin G, Marinelli F, Forrest LR, Chen H, Chipot C, Kohlmeyer A, Santuz H, Hénin J) J Phys Chem B 2024 Nov 14;128(45):11108-11123 PMID: 39501453 PMCID: PMC11572706 SCOPUS ID: 2-s2.0-85208394452 11/06/2024       15 Citations
  • Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity. (Marinelli F, Faraldo-Gómez JD) Proc Natl Acad Sci U S A 2024 Apr 16;121(16):e2318009121 PMID: 38588414 PMCID: PMC11032461 SCOPUS ID: 2-s2.0-85190324798 04/08/2024       8 Citations
  • Conformational free-energy landscapes of a Na+/Ca2+ exchanger explain its alternating-access mechanism and functional specificity. (Marinelli F, Faraldo-Gómez JD) bioRxiv 2023 Oct 21 PMID: 36789408 PMCID: PMC9928037 02/16/2023    
  • Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+ channel TMEM175. (Oh S, Marinelli F, Zhou W, Lee J, Choi HJ, Kim M, Faraldo-Gómez JD, Hite RK) Elife 2022 May 24;11 PMID: 35608336 PMCID: PMC9129878 SCOPUS ID: 2-s2.0-85130675029 05/25/2022       20 Citations
  • Force-Correction Analysis Method for Derivation of Multidimensional Free-Energy Landscapes from Adaptively Biased Replica Simulations. (Marinelli F, Faraldo-Gómez JD) J Chem Theory Comput 2021 Nov 09;17(11):6775-6788 PMID: 34669402 SCOPUS ID: 2-s2.0-85118805062 10/21/2021       6 Citations
  • Interpreting Hydrogen-Deuterium Exchange Experiments with Molecular Simulations: Tutorials and Applications of the HDXer Ensemble Reweighting Software [Article v1.0]. (Lee PS, Bradshaw RT, Marinelli F, Kihn K, Smith A, Wintrode PL, Deredge DJ, Faraldo-Gómez JD, Forrest LR) Living J Comput Mol Sci 2021;3(1) PMID: 36644498 PMCID: PMC9835200 01/01/2021    
  • Interpretation of HDX Data by Maximum-Entropy Reweighting of Simulated Structural Ensembles. (Bradshaw RT, Marinelli F, Faraldo-Gómez JD, Forrest LR) Biophys J 2020 Apr 07;118(7):1649-1664 PMID: 32105651 PMCID: PMC7136279 SCOPUS ID: 2-s2.0-85080084845 02/28/2020       29 Citations
  • Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics. (Fiorin G, Marinelli F, Faraldo-Gómez JD) J Comput Chem 2020 Feb 15;41(5):449-459 PMID: 31602694 PMCID: PMC8388148 SCOPUS ID: 2-s2.0-85074051447 10/12/2019       28 Citations
  • Promoting transparency and reproducibility in enhanced molecular simulations. (PLUMED consortium) Nat Methods 2019 Aug;16(8):670-673 PMID: 31363226 SCOPUS ID: 2-s2.0-85069961147 08/01/2019       845 Citations
  • Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP. (Li M, Wang Y, Banerjee R, Marinelli F, Silberberg S, Faraldo-Gómez JD, Hattori M, Swartz KJ) Elife 2019 Jun 24;8 PMID: 31232692 PMCID: PMC6590987 SCOPUS ID: 2-s2.0-85071880082 06/25/2019       8 Citations
  • Structural Characterization of Biomolecules through Atomistic Simulations Guided by DEER Measurements. (Marinelli F, Fiorin G) Structure 2019 Feb 05;27(2):359-370.e12 PMID: 30528595 PMCID: PMC6860373 SCOPUS ID: 2-s2.0-85060735246 12/12/2018       18 Citations
  • Confidence Analysis of DEER Data and Its Structural Interpretation with Ensemble-Biased Metadynamics. (Hustedt EJ, Marinelli F, Stein RA, Faraldo-Gómez JD, Mchaourab HS) Biophys J 2018 Oct 02;115(7):1200-1216 PMID: 30197182 PMCID: PMC6170522 SCOPUS ID: 2-s2.0-85052928173 09/11/2018       41 Citations
  • The prokaryotic Na+/Ca2+ exchanger NCX_Mj transports Na+ and Ca2+ in a 3:1 stoichiometry. (Shlosman I, Marinelli F, Faraldo-Gómez JD, Mindell JA) J Gen Physiol 2018 Jan 02;150(1):51-65 PMID: 29237756 PMCID: PMC5749117 SCOPUS ID: 2-s2.0-85039953929 12/15/2017       26 Citations
  • Atomistic simulations indicate the c-subunit ring of the F1Fo ATP synthase is not the mitochondrial permeability transition pore. (Zhou W, Marinelli F, Nief C, Faraldo-Gómez JD) Elife 2017 Feb 10;6 PMID: 28186490 PMCID: PMC5323039 SCOPUS ID: 2-s2.0-85014079638 02/12/2017       73 Citations
  • Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger. (Liao J, Marinelli F, Lee C, Huang Y, Faraldo-Gómez JD, Jiang Y) Nat Struct Mol Biol 2016 Jun;23(6):590-599 PMID: 27183196 PMCID: PMC4918766 SCOPUS ID: 2-s2.0-84968658964 05/18/2016       80 Citations
  • Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg(2+) through the SOMA string method. (Branduardi D, Marinelli F, Faraldo-Gómez JD) J Comput Chem 2016 Mar 05;37(6):575-86 PMID: 26149527 SCOPUS ID: 2-s2.0-84959527999 07/08/2015       10 Citations
  • Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions. (Marinelli F, Faraldo-Gómez JD) Biophys J 2015 Jun 16;108(12):2779-82 PMID: 26083917 PMCID: PMC4472218 SCOPUS ID: 2-s2.0-84931269561 06/18/2015       61 Citations
  • Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation. (Marinelli F, Almagor L, Hiller R, Giladi M, Khananshvili D, Faraldo-Gómez JD) Proc Natl Acad Sci U S A 2014 Dec 16;111(50):E5354-62 PMID: 25468964 PMCID: PMC4273333 SCOPUS ID: 2-s2.0-84919343757 12/04/2014       64 Citations
  • Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism. (Marinelli F) Biophys J 2013 Sep 03;105(5):1236-47 PMID: 24010667 PMCID: PMC3817379 SCOPUS ID: 2-s2.0-84883607162 09/10/2013       17 Citations
  • Two-state dynamics of the SH3-SH2 tandem of Abl kinase and the allosteric role of the N-cap. (Corbi-Verge C, Marinelli F, Zafra-Ruano A, Ruiz-Sanz J, Luque I, Faraldo-Gómez JD) Proc Natl Acad Sci U S A 2013 Sep 03;110(36):E3372-80 PMID: 23959873 PMCID: PMC3767523 SCOPUS ID: 2-s2.0-84883405702 08/21/2013       36 Citations
  • Molecular description of the propagation of chirality from molecules to complex systems: different mechanisms controlled by hydrophobic interactions. (Marinelli F, Sorrenti A, Corvaglia V, Leone V, Mancini G) Chemistry 2012 Nov 12;18(46):14680-8 PMID: 23019089 SCOPUS ID: 2-s2.0-84868688876 09/29/2012       19 Citations
  • METAGUI. A VMD interface for analyzing metadynamics and molecular dynamics simulations (Biarnés X, Pietrucci F, Marinelli F, Laio A) Computer Physics Communications January 2012;183(1):203-211 SCOPUS ID: 2-s2.0-80055015114 01/01/2012       84 Citations
  • Evidence for an allosteric mechanism of substrate release from membrane-transporter accessory binding proteins. (Marinelli F, Kuhlmann SI, Grell E, Kunte HJ, Ziegler C, Faraldo-Gómez JD) Proc Natl Acad Sci U S A 2011 Dec 06;108(49):E1285-92 PMID: 22084072 PMCID: PMC3241785 SCOPUS ID: 2-s2.0-83755178463 11/16/2011       27 Citations
  • Metadynamics convergence law in a multidimensional system. (Crespo Y, Marinelli F, Pietrucci F, Laio A) Phys Rev E Stat Nonlin Soft Matter Phys 2010 May;81(5 Pt 2):055701 PMID: 20866290 09/28/2010    
  • Targeting biomolecular flexibility with metadynamics. (Leone V, Marinelli F, Carloni P, Parrinello M) Curr Opin Struct Biol 2010 Apr;20(2):148-54 PMID: 20171876 SCOPUS ID: 2-s2.0-77951294588 02/23/2010       134 Citations
  • Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model. (Cossio P, Marinelli F, Laio A, Pietrucci F) J Phys Chem B 2010 Mar 11;114(9):3259-65 PMID: 20163137 SCOPUS ID: 2-s2.0-77749316142 02/19/2010       37 Citations
  • PLUMED: A portable plugin for free-energy calculations with molecular dynamics (Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, Donadio D, Marinelli F, Pietrucci F, Broglia RA, Parrinello M) Computer Physics Communications October 2009;180(10):1961-1972 SCOPUS ID: 2-s2.0-69349100797 10/01/2009       1543 Citations
  • A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations. (Marinelli F, Pietrucci F, Laio A, Piana S) PLoS Comput Biol 2009 Aug;5(8):e1000452 PMID: 19662155 PMCID: PMC2711228 SCOPUS ID: 2-s2.0-69049099679 08/08/2009       243 Citations
  • Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations. (Pietrucci F, Marinelli F, Carloni P, Laio A) J Am Chem Soc 2009 Aug 26;131(33):11811-8 PMID: 19645490 SCOPUS ID: 2-s2.0-69049084558 08/04/2009       132 Citations
  • Exploring the folding free energy landscape of insulin using bias exchange metadynamics. (Todorova N, Marinelli F, Piana S, Yarovsky I) J Phys Chem B 2009 Mar 19;113(11):3556-64 PMID: 19243106 SCOPUS ID: 2-s2.0-65249172627 02/27/2009       42 Citations
  • Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants. (Piana S, Laio A, Marinelli F, Van Troys M, Bourry D, Ampe C, Martins JC) J Mol Biol 2008 Jan 11;375(2):460-70 PMID: 18022635 SCOPUS ID: 2-s2.0-36548999391 11/21/2007       44 Citations
  • Theoretical prediction of thermodynamic equilibrium constants of chemical reactions in water (D'Abramo M, Aschi M, Marinelli F, Di Nola A, Amadei A) Journal of Molecular Structure THEOCHEM 1 June 2007;811(1-3):197-201 SCOPUS ID: 2-s2.0-34248173815 06/01/2007       3 Citations
  • Ground and excited electronic state thermodynamics of aqueous carbon monoxide: a theoretical study. (D'Alessandro M, Marinelli F, D'Abramo M, Aschi M, Di Nola A, Amadei A) J Chem Phys 2005 Mar 22;122(12):124507 PMID: 15836397 SCOPUS ID: 2-s2.0-17444418604 04/20/2005       6 Citations
  • Theoretical modeling of vibroelectronic quantum states in complex molecular systems: solvated carbon monoxide, a test case. (Amadei A, Marinelli F, D'Abramo M, D'Alessandro M, Anselmi M, Di Nola A, Aschi M) J Chem Phys 2005 Mar 22;122(12):124506 PMID: 15836396 SCOPUS ID: 2-s2.0-17444426056 04/20/2005       32 Citations
    • Last update: 10/12/2025