Massimiliano Bonomi

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michele parrinelloDepartment of ChemistryVerified email at phys.chem.ethz.ch
Carlo CamilloniUniversity of MilanoVerified email at unimi.it
Michele VendruscoloProfessor of Biophysics, University of CambridgeVerified email at cam.ac.uk
Alessandro BarducciCentre de Biologie Structurale (CBS), Montpellier, FranceVerified email at cbs.cnrs.fr
Andrej SaliUniversity of California, San FranciscoVerified email at salilab.org
Davide BranduardiComputational Chemistry & Informatics Group at AstexVerified email at astx.com
Giovanni BussiScuola Internazionale Superiore di Studi Avanzati, Trieste, ItalyVerified email at sissa.it
Avner SchlessingerProfessor, Icahn School of Medicine at Mount Sinai, New York, NYVerified email at mssm.edu
Gabriella T HellerUniversity College LondonVerified email at ucl.ac.uk
Davide ProvasiMount Sinai School of Medicine, New YorkVerified email at mssm.edu
Jim PfaendtnerUniversity of WashingtonVerified email at uw.edu
Gareth TribelloSchool of Maths and Physics, Queen's University BelfastVerified email at qub.ac.uk
Francesco Luigi GervasioProfessor of Pharmaceutical Sciences at University of Geneva & Professor of Chemistry UCLVerified email at unige.ch
Thomas LöhrSenior Scientist, AstraZenecaVerified email at astrazeneca.com
Charles GreenbergUniversity of California, San FranciscoVerified email at ucsf.edu
Davide DonadioUniversity of California DavisVerified email at ucdavis.edu
Fabio Pietrucciassociate professor (maître de conférences, HDR), Sorbonne UniversitéVerified email at sorbonne-universite.fr
Professor Paolo Raiteri, PhDCurtin UniversityVerified email at curtin.edu.au
Fabrizio MarinelliStaff Scientist, National Institutes of Health, USAVerified email at nih.gov
Vittorio LimongelliUSI Lugano (Switzerland)Verified email at usi.ch

Massimiliano Bonomi

Institut Pasteur, CNRS

Verified email at pasteur.fr - Homepage

Computational Structural Biology Integrative Structural Biology Molecular Modelling


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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	2548	2014
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	1626	2009
Metadynamics A Barducci, M Bonomi, M Parrinello Wiley Interdisciplinary Reviews: Computational Molecular Science, 2011	1351*	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	553	2019
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	360	2013
Reconstructing the equilibrium Boltzmann distribution from well‐tempered metadynamics M Bonomi, A Barducci, M Parrinello Journal of computational chemistry 30 (11), 1615-1621, 2009	346	2009
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	341*	2022
Principles of protein structural ensemble determination M Bonomi, GT Heller, C Camilloni, M Vendruscolo Current opinion in structural biology 42, 106-116, 2017	284	2017
Enhanced sampling in the well-tempered ensemble M Bonomi, M Parrinello Physical review letters 104 (19), 190601, 2010	266	2010
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	254	2019
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	246	2013
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	227	2010
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	185	2015
Metainference: A Bayesian inference method for heterogeneous systems M Bonomi, C Camilloni, A Cavalli, M Vendruscolo Science advances 2 (1), e1501177, 2016	176	2016
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	135	2012
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	121	2015
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	119	2014
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	117	2017
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	107	2008
Integrative structure modeling with the Integrative Modeling Platform B Webb, S Viswanath, M Bonomi, R Pellarin, CH Greenberg, D Saltzberg, ... Protein Science 27 (1), 245-258, 2018	97	2018

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