Massimiliano Bonomi
Massimiliano Bonomi
Verified email at pasteur.fr - Homepage
TitleCited byYear
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
M Bonomi, D Branduardi, G Bussi, C Camilloni, D Provasi, P Raiteri, ...
Computer Physics Communications 180 (10), 1961-1972, 2009
10212009
PLUMED 2: New feathers for an old bird
GA Tribello, M Bonomi, D Branduardi, C Camilloni, G Bussi
Computer Physics Communications 185 (2), 604-613, 2014
9122014
Metadynamics
A Barducci, M Bonomi, M Parrinello
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011
672*2011
Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics
M Bonomi, A Barducci, M Parrinello
Journal of computational chemistry 30 (11), 1615-1621, 2009
2342009
Funnel metadynamics as accurate binding free-energy method
V Limongelli, M Bonomi, M Parrinello
Proceedings of the National Academy of Sciences 110 (16), 6358-6363, 2013
1902013
Enhanced sampling in the well-tempered ensemble
M Bonomi, M Parrinello
Physical review letters 104 (19), 190601, 2010
1822010
Crystal structure of a eukaryotic phosphate transporter
BP Pedersen, H Kumar, AB Waight, AJ Risenmay, Z Roe-Zurz, BH Chau, ...
Nature 496 (7446), 533, 2013
1752013
Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition
V Limongelli, M Bonomi, L Marinelli, FL Gervasio, A Cavalli, E Novellino, ...
Proceedings of the National Academy of Sciences 107 (12), 5411-5416, 2010
1602010
Principles of protein structural ensemble determination
M Bonomi, GT Heller, C Camilloni, M Vendruscolo
Current opinion in structural biology 42, 106-116, 2017
972017
The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin
M Bonomi, D Branduardi, FL Gervasio, M Parrinello
Journal of the American Chemical Society 130 (42), 13938-13944, 2008
932008
Efficient simulation of explicitly solvated proteins in the well-tempered ensemble
M Deighan, M Bonomi, J Pfaendtner
Journal of chemical theory and computation 8 (7), 2189-2192, 2012
862012
Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ
KS Molnar, M Bonomi, R Pellarin, GD Clinthorne, G Gonzalez, ...
Structure 22 (9), 1239-1251, 2014
802014
Accuracy of current all-atom force-fields in modeling protein disordered states
F Palazzesi, MK Prakash, M Bonomi, A Barducci
Journal of chemical theory and computation 11 (1), 2-7, 2014
772014
Metainference: A Bayesian inference method for heterogeneous systems
M Bonomi, C Camilloni, A Cavalli, M Vendruscolo
Science Advances 2 (1), e1501177, 2016
692016
Efficient sampling of high-dimensional free-energy landscapes with parallel bias metadynamics
J Pfaendtner, M Bonomi
Journal of chemical theory and computation 11 (11), 5062-5067, 2015
692015
Free-energy landscape of protein oligomerization from atomistic simulations
A Barducci, M Bonomi, MK Prakash, M Parrinello
Proceedings of the National Academy of Sciences 110 (49), E4708-E4713, 2013
632013
Structural basis for alternating access of a eukaryotic calcium/proton exchanger
AB Waight, BP Pedersen, A Schlessinger, M Bonomi, BH Chau, ...
Nature 499 (7456), 107, 2013
632013
Simultaneous quantification of protein order and disorder
P Sormanni, D Piovesan, GT Heller, M Bonomi, P Kukic, C Camilloni, ...
Nature chemical biology 13 (4), 339, 2017
512017
Linking well-tempered metadynamics simulations with experiments
A Barducci, M Bonomi, M Parrinello
Biophysical journal 98 (9), L44-L46, 2010
502010
Insight into the folding inhibition of the HIV-1 protease by a small peptide
M Bonomi, FL Gervasio, G Tiana, D Provasi, RA Broglia, M Parrinello
Biophysical journal 93 (8), 2813-2821, 2007
452007
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Articles 1–20