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Massimiliano Bonomi
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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
31672014
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
18652009
Metadynamics
A Barducci, M Bonomi, M Parrinello
Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011
1582*2011
Promoting transparency and reproducibility in enhanced molecular simulations
M Bonomi, G Bussi, C Camilloni, GA Tribello, P Banas, A Barducci, ...
Nature Methods 16 (8), 670-673, 2019
8112019
Bat coronaviruses related to SARS-CoV-2 and infectious for human cells
S Temmam, K Vongphayloth, E Baquero, S Munier, M Bonomi, ...
Nature 604 (7905), 330-336, 2022
508*2022
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
4342013
Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics
M Bonomi, A Barducci, M Parrinello
Journal of computational chemistry 30 (11), 1615-1621, 2009
3922009
Effects of α-tubulin acetylation on microtubule structure and stability
L Eshun-Wilson, R Zhang, D Portran, MV Nachury, DB Toso, T Löhr, ...
Proceedings of the National Academy of Sciences 116 (21), 10366-10371, 2019
3362019
Principles of protein structural ensemble determination
M Bonomi, GT Heller, C Camilloni, M Vendruscolo
Current opinion in structural biology 42, 106-116, 2017
3352017
Enhanced sampling in the well-tempered ensemble
M Bonomi, M Parrinello
Physical review letters 104 (19), 190601, 2010
2872010
Crystal structure of a eukaryotic phosphate transporter
BP Pedersen, H Kumar, AB Waight, AJ Risenmay, Z Roe-Zurz, BH Chau, ...
Nature 496 (7446), 533-536, 2013
2662013
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
2542010
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
2382015
Metainference: A Bayesian inference method for heterogeneous systems
M Bonomi, C Camilloni, A Cavalli, M Vendruscolo
Science advances 2 (1), e1501177, 2016
2222016
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
1512012
Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease
GT Heller, FA Aprile, TCT Michaels, R Limbocker, M Perni, FS Ruggeri, ...
Science advances 6 (45), eabb5924, 2020
1382020
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, 2015
1322015
Simultaneous quantification of protein order and disorder
P Sormanni, D Piovesan, GT Heller, M Bonomi, P Kukic, C Camilloni, ...
Nature chemical biology 13 (4), 339-342, 2017
1262017
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
1262014
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
1112008
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