Massimiliano Bonomi

According to our database, Massimiliano Bonomi authored at least 10 papers between 2009 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.

Samuel E. Hoff, F. Emil Thomasen, Kresten Lindorff-Larsen, Massimiliano Bonomi

PLoS Comput. Biol., 2024

2022

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design.

Francesco P. Panei, Rachel Torchet, Hervé Ménager, Paraskevi Gkeka, Massimiliano Bonomi

Bioinform., 2022

2020

What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data?

James S. Fraser, Kresten Lindorff-Larsen, Massimiliano Bonomi

J. Chem. Inf. Model., 2020

2017

Integrative structural and dynamical biology with PLUMED-ISDB.

Massimiliano Bonomi, Carlo Camilloni

Bioinform., 2017

2015

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening.

Claire Colas, Christof Grewer, Nicholas James Otte, Armanda Gameiro, Thomas Albers, Kurnvir Singh, Helen Shere, Massimiliano Bonomi, Jeff Holst, Avner Schlessinger

PLoS Comput. Biol., 2015

2014

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery.

Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson

PLoS Comput. Biol., 2014

PLUMED 2: New feathers for an old bird.

Gareth A. Tribello, Massimiliano Bonomi, Davide Branduardi, Carlo Camilloni, Giovanni Bussi

Comput. Phys. Commun., 2014

2011

A chirality-based metrics for free-energy calculations in biomolecular systems.

Adriana Pietropaolo, Davide Branduardi, Massimiliano Bonomi, Michele Parrinello

J. Comput. Chem., 2011

2009

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

Massimiliano Bonomi, Alessandro Barducci, Michele Parrinello

J. Comput. Chem., 2009

PLUMED: A portable plugin for free-energy calculations with molecular dynamics.

Massimiliano Bonomi, Davide Branduardi, Giovanni Bussi, Carlo Camilloni, Davide Provasi, Paolo Raiteri, Davide Donadio, Fabrizio Marinelli, Fabio Pietrucci, Ricardo A. Broglia, Michele Parrinello

Comput. Phys. Commun., 2009