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Massimiliano Bonomi

computational structural biology unit

45H-index
148Paper Count
1.6WCitation Count
Published Papers 60
Publication Date
From possibility to precision in macromolecular ensemble prediction
err2026-05-18
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PREAI
errStephanie A. Wankowicz; Massimiliano Bonomi
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Making PLUMED Fly: A Tutorial on Optimizing Performance
err2026-02-24
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errOAAI
errDaniele Rapetti; Massimiliano Bonomi; Carlo Camilloni; Giovanni Bussi; Gareth A. Tribello
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Atomic resolution ensembles of intrinsically disordered proteins with Alphafold
err2026-02-05
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errOAAI
errVincent Schnapka; Tatiana I. Morozova; Samiran Sen; Massimiliano Bonomi
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Determining accurate conformational ensembles of intrinsically disordered proteins at atomic resolution
err2025-10-10
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errOAAI
errKaushik Borthakur; Thomas R. Sisk; Francesco P. Panei; Massimiliano Bonomi; Paul Robustelli
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Small molecule dysregulation of ClpP activity via bidirectional allosteric pathways
err2025-08-11
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PREAI
errMarim M. Barghash; Mark F. Mabanglo; Samuel E. Hoff; Dmytro Brozdnychenko; Keith S. Wong; Gursonika Binepal; Philbert Ip; Jiarui Shen; Tomohiro Furukawa; Hidekazu Katayama; Vincent Trudel; Joanne Tan; Andrei K. Yudin; Scott D. Gray-Owen; Shohei Sakuda; Robert A. Batey; Siavash Vahidi; Massimiliano Bonomi; Walid A. Houry
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Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations
err2025-05-16
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errOAAI
errPosani, Elisa; Janos, Pavel; Haack, Daniel; Toor, Navtej; Bonomi, Massimiliano; Magistrato, Alessandra; Bussi, Giovanni
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PLUMED Tutorials: A collaborative, community-driven learning ecosystem
err2025-03-07
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PREAI
errTribello, Gareth A.; Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Armstrong, Blake I.; Arsiccio, Andrea; Aureli, Simone; Ballabio, Federico; Bernetti, Mattia; Bonati, Luigi; Brookes, Samuel G. H.; Brotzakis, Z. Faidon; Capelli, Riccardo; Ceriotti, Michele; Chan, Kam-Tung; Cossio, Pilar; Dasetty, Siva; Donadio, Davide; Ensing, Bernd; Ferguson, Andrew L.; Fraux, Guillaume; Gale, Julian D.; Gervasio, Francesco Luigi; Giorgino, Toni; Herringer, Nicholas S. M.; Hocky, Glen M.; Hoff, Samuel E.; Invernizzi, Michele; Languin-Cattoen, Olivier; Leone, Vanessa; Limongelli, Vittorio; Lopez-Acevedo, Olga; Marinelli, Fabrizio; Febrer Martinez, Pedro; Masetti, Matteo; Mehdi, Shams; Michaelides, Angelos; Murtada, Mhd Hussein; Parrinello, Michele; Piaggi, Pablo M.; Pietropaolo, Adriana; Pietrucci, Fabio; Pipolo, Silvio; Pritchard, Claire; Raiteri, Paolo; Raniolo, Stefano; Rapetti, Daniele; Rizzi, Valerio; Rydzewski, Jakub; Salvalaglio, Matteo; Schran, Christoph; Seal, Aniruddha; Shayesteh Zadeh, Armin; Silva, Tomas F. D.; Spiwok, Vojtech; Stirnemann, Guillaume; Sucerquia, Daniel; Tiwary, Pratyush; Valsson, Omar; Vendruscolo, Michele; Voth, Gregory A.; White, Andrew D.; Wu, Jiangbo
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Bonds and bytes: The odyssey of structural biology
err2024-02-01
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errOAAI
errHoff, S. E.; Zinke, M.; Izadi-Pruneyre, N.; Bonomi, M.
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Genotype and Phenotype Characterization of Rhinolophus sp. Sarbecoviruses from Vietnam: Implications for Coronavirus Emergence
err2023-09-08
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errOAAI
errTemmam, Sarah; Tu, Tran Cong; Regnault, Beatrice; Bonomi, Massimiliano; Chretien, Delphine; Vendramini, Lea; Duong, Tran Nhu; Phong, Tran Vu; Yen, Nguyen Thi; Anh, Hoang Ngoc; Son, Tran Hai; Anh, Pham Tuan; Amara, Faustine; Bigot, Thomas; Munier, Sandie; Thong, Vu Dinh; van der Werf, Sylvie; Nam, Vu Sinh; Eloit, Marc
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Clustering Heterogeneous Conformational Ensembles of Intrinsically Disordered Proteins with t-Distributed Stochastic Neighbor Embedding
err2023-06-20
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errOAAI
errAppadurai, Rajeswari; Koneru, Jaya Krishna; Bonomi, Massimiliano; Robustelli, Paul; Srivastava, Anand
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Virus Pop-Expanding Viral Databases by Protein Sequence Simulation
err2023-05-24
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errOAAI
errKende, Julia; Bonomi, Massimiliano; Temmam, Sarah; Regnault, Beatrice; Perot, Philippe; Eloit, Marc; Bigot, Thomas
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SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19
err2023-03-06
err10
PREAI
errTemmam, Sarah; Montagutelli, Xavier; Herate, Cecile; Donati, Flora; Regnault, Beatrice; Attia, Mikael; Salazar, Eduard Baquero; Chretien, Delphine; Conquet, Laurine; Jouvion, Gregory; Da Fonseca, Juliana Pipoli; Cokelaer, Thomas; Amara, Faustine; Relouzat, Francis; Naninck, Thibaut; Lemaitre, Julien; Derreudre-Bosquet, Nathalie; Pascal, Quentin; Bonomi, Massimiliano; Bigot, Thomas; Munier, Sandie; Rey, Felix A.; Le Grand, Roger; van Der Werf, Sylvie; Eloit, Marc
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Describing inhibitor specificity for the amino acid transporter LAT1 from metainference simulations
err2022-12-01
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errOAAI
errHutchinson, Keino; Silva, Dina Buitrago; Bohlke, Joshua; Clausen, Chase; Thomas, Allen A.; Bonomi, Massimiliano; Schlessinger, Avner
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Exploring the conformational diversity of proteins
err2022-04-21
err10
errOAAI
errSchlessinger, Avner; Bonomi, Massimiliano
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Editorial: Experiments and Simulations: A Pas de Deux to Unravel Biological Function
err2021-11-29
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errOAAI
errTopf, Maya; Rosta, Edina; Bowman, Gregory R.; Bonomi, Massimiliano
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Rational design of ASCT2 inhibitors using an integrated experimental-computational approach
err2021-09-10
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errOAAI
errGaribsingh, Rachel-Ann A.; Ndaru, Elias; Garaeva, Alisa A.; Shi, Yueyue; Zielewicz, Laura; Zakrepine, Paul; Bonomi, Massimiliano; Slotboom, Dirk J.; Paulino, Cristina; Grewer, Christof; Schlessinger, Avner
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Multi-replica biased sampling for photoswitchable π-conjugated polymers
err2021-05-05
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errOAAI
errFortino, Mariagrazia; Cozza, Concetta; Bonomi, Massimiliano; Pietropaolo, Adriana
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Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease
err2020-11-06
err95
errOAAI
errHeller, Gabriella T.; Aprile, Francesco A.; Michaels, Thomas C. T.; Limbocker, Ryan; Perni, Michele; Ruggeri, Francesco Simone; Mannini, Benedetta; Lohr, Thomas; Bonomi, Massimiliano; Camilloni, Carlo; De Simone, Alfonso; Felli, Isabella C.; Pierattelli, Roberta; Knowles, Tuomas P. J.; Dobson, Christopher M.; Vendruscolo, Michele
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