All Pages

V. Babin, C. Roland, and C. Sagui. Adaptively biased molecular dynamics for free energy calculations. J. Chem. Phys., 128:134101, 2008.


Fahimeh Baftizadeh, Pilar Cossio, Fabio Pietrucci, and Alessandro Laio. Protein folding and ligand-enzyme binding from bias-exchange metadynamics simulations. Curr Phys Chem, 2:79–91, 2012.


A Barducci, G Bussi, and M Parrinello. Well-tempered metadynamics: A smoothly converging and tunable free-energy method. Phys. Rev. Lett., 100(2):020603, Jan 2008.


Alessandro Barducci, Massimiliano Bonomi, and Michele Parrinello. Metadynamics. Wiley Interdisciplinary Reviews: Computational Molecular Science, 1(5):826–843, 2011.


C. Bartels and M. Karplus. Probability Distributions for Complex Systems: Adaptive Umbrella Sampling of the Potential Energy. J. Phys. Chem. B, 102(5):865–880, 1998.


M. Bonomi and M. Parrinello. Enhanced sampling in the well-tempered ensemble. Phys. Rev. Lett., 104:190601, 2010.


Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Davide Provasi, Paolo Raiteri, Davide Donadio, Fabrizio Marinelli, Fabio Pietrucci, Ricardo A Broglia, and Michele Parrinello. PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Computer Physics Communications, 180(10):1961–1972, 2009.


Wouter Boomsma, Kresten Lindorff-Larsen, and Jesper Ferkinghoff-Borg. Combining Experiments and Simulations Using the Maximum Entropy Principle. PLoS Comput. Biol., 10(2):e1003406, February 2014.


Davide Branduardi, Francesco Luigi Gervasio, and Michele Parrinello. From A to B in free energy space. J. Chem. Phys., 126(5):054103, Feb 2007.


D Branduardi, G Bussi, and M PARRINELLO. Metadynamics with adaptive Gaussians. J. Chem. Theory Comput., 8(7):2247–2254, 2012.


Giovanni Bussi, Francesco Luigi Gervasio, Alessandro Laio, and Michele Parrinello. Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J. Am. Chem. Soc., 128(41):13435–41, 2006.


Carlo Camilloni and Michele Vendruscolo. Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics. J. Am. Chem. Soc., 136(25):8982–8991, June 2014.


C. Camilloni, R. A. Broglia, and G. Tiana. Hierarchy of folding and unfolding events of protein g, ci2, and acbp from explicit-solvent simulations. J. Chem. Phys., 134:045105, 2011.


Carlo Camilloni, Paul Robustelli, Alfonso De Simone, Andrea Cavalli, and Michele Vendruscolo. Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts. J. Am. Chem. Soc., 134(9):3968–3971, 2012.


Carlo Camilloni, Andrea Cavalli, and Michele Vendruscolo. Replica-Averaged Metadynamics. J. Chem. Theory Comput., 9(12):5610–5617, December 2013.


Carlo Camilloni, Andrea Cavalli, and Michele Vendruscolo. Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins. J. Phys. Chem. B, 117(6):1838–1843, 2013.


Andrea Cavalli, Carlo Camilloni, and Michele Vendruscolo. Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle. J. Chem. Phys., 138(9):094112, March 2013.


Michael Deighan, Massimiliano Bonomi, and Jim Pfaendtner. Efficient simulation of explicitly solvated proteins in the well-tempered ensemble. Journal of Chemical Theory and Computation, 8(7):2189–2192, 2012.


Trang N. Do, Paolo Carloni, Gabriele Varani, and Giovanni Bussi. Rna/peptide binding driven by electrostatics—insight from bidirectional pulling simulations. Journal of Chemical Theory and Computation, 9(3):1720–1730, 2013.


Alejandro Gil-Ley and Giovanni Bussi. Enhanced conformational sampling using replica exchange with collective-variable tempering. Journal of chemical theory and computation, 11(3):1077–1085, 2015.


Daniele Granata, Carlo Camilloni, Michele Vendruscolo, and Alessandro Laio. Characterization of the free-energy landscapes of proteins by NMR-guided metadynamics. Proc. Natl. Acad. Sci. U.S.A., 110(17):6817–6822, 2013.


H. Grubmüller, B. A. Heymann, and P. Tavan. Science, 271:997–999, 1996.


C. Jarzynski. Nonequilibrium equality for free energy differences. Phys. Rev. Lett., 78:2690–2693, 1997.


S. K. Kearsley. On the orthogonal transformation used for structural comparison. Acta Cryst. A, 45:208–210, 1989.


KJ Kohlhoff, Paul Robustelli, Andrea Cavalli, Xavier Salvatella, and Michele Vendruscolo. Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J. Am. Chem. Soc., 131(39):13894–13895, 2009.


Alessandrio Laio and Francesco Luigi Gervasio. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep. Prog. Phys., 71:126601, 2008.


A. Laio and M. Parrinello. Escaping free energy minima. Proc. Natl. Acad. Sci. USA, 99:12562–12566, 2002.


Wolfgang Lechner and Christoph Dellago. Accurate determination of crystal structures based on averaged local bond order parameters. The Journal of Chemical Physics, 129(11):–, 2008.


M. Marchi and P. Ballone. Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems. J. Chem. Phys., 110(8):3697–3702, 1999.


Stefano Piana and Alessandro Laio. A bias-exchange approach to protein folding. J. Phys. Chem. B, 111(17):4553–9, 2007.


F. Pietrucci and A. Laio. A collective variable for the efficient exploration of protein beta-structures with metadynamics: application to sh3 and gb1. J. Chem. Theory Comput., 5(9):2197–2201, 2009.


D. Provasi and M. Filizola. Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics. Biophys. J., 98:2347––2355, 2010.


P. Raiteri, A. Laio, F.L. Gervasio, C. Micheletti, and M. Parrinello. Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. J. Phys. Chem. B, 110:3533–3539, 2006.


Paul Robustelli, Kai Kohlhoff, Andrea Cavalli, and Michele Vendruscolo. Using NMR chemical shifts as structural restraints in molecular dynamics simulations of proteins. Structure, 18(8):923–933, 2010.


Aleksandr B Sahakyan, Wim F Vranken, Andrea Cavalli, and Michele Vendruscolo. Structure-based prediction of methyl chemical shifts in proteins. J. Biomol. NMR, 50(4):331–346, 2011.


Vojtech Spiwok and Blanka Králová. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap. Journal of Chemical Physics, 135(22):224504, December 2011.


Yuji Sugita and Yuko Okamoto. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett., 314(1–2):141–151, November 1999.


Ludovico Sutto, Simone Marsili, and Francesco Luigi Gervasio. New advances in metadynamics. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2(5):771–779, 2012.


Pratyush Tiwary and Michele Parrinello. From metadynamics to dynamics. Phys. Rev. Lett., 111:230602, Dec 2013.


G.M. Torrie and J.P. Valleau. Nonphysical sampling distributions in monte carlo free energy estimation: Umbrella sampling. J. Comput. Phys., 23:187–199, 1977.


Gareth A. Tribello, Jérôme Cuny, Hagai Eshet, and Michele Parrinello. Exploring the free energy surfaces of clusters using reconnaissance metadynamics. J. Chem. Phys., 135(11):114109, 2011.


Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, and Giovanni Bussi. Plumed 2: New feathers for an old bird. Comput. Phys. Commun., 185(2):604–613, 2014.


Ji v rí Vym v etal and Ji v rí Vondrá v sek. Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Folding. J. Phys. Chem. A, page 110930112611005, 2011.