Author

M. Bonomi

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biophysics· 5 Biochemistry· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 4 Research Focus:drug response / drug discovery· 4 Approach:statistical model· 4 Assay:cryo-EM· 3 Approach:experimental assay· 2 Organism:human· 2 Research Focus:protein folding & dynamics· 2 Assay:proteomics· 2

Frequent Co-Authors

M. Vendruscolo· 3 shared A. Schlessinger· 2 shared T. Lohr· 2 shared A. A. Garaeva· 1 shared A. A. Thomas· 1 shared A. De Simone· 1 shared A. Srivastava· 1 shared B. Mannini· 1 shared

Activity by Year

2019-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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3 shared papersBiophysics

M. Vendruscolo

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Author profile →

6 papers

Recent·Most cited

Clustering conformational ensembles of intrinsically disordered proteins with t-distributed stochastic neighbor embedding

R. Appadurai, J. Krishna, M. Bonomi, P. Robustelli, A. Srivastava

This paper uses t-SNE to cluster conformations of intrinsically disordered proteins, revealing structurally similar groups and insights into ligand binding mechanisms.

bioRxiv · Nov 11, 2022 · PreprintBiophysics

Determination of the structure and dynamics of the fuzzy coat of an amyloid fibril of IAPP using cryo-electron microscopy

Z. F. Brotzakis, T. Löhr, S. Truong, S. E. Hoff, M. Bonomi, M. Vendruscolo

The paper develops MEMMI, a cryo-EM method that determines structure and dynamics of large systems, and applies it to study the fuzzy coat of an IAPP amyloid fibril.

bioRxiv · May 29, 2022Biophysics

Describing Inhibitor Specificity for the Amino Acid Transporter LAT1 from Metainference Simulations

K. Hutchinson, D. B. Silva, J. Bohlke, C. Clausen, A. A. Thomas, M. Bonomi, A. Schlessinger

This study uses metainference MD simulations, molecular docking, and experiments to identify critical residues and druggable pockets in LAT1, leading to the discovery of new inhibitors.

bioRxiv · May 3, 2022Biophysics

Small molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer's disease

G. T. Heller, F. A. Aprile, T. C. Michaels, R. Limbocker, M. Perni, F. S. Ruggeri, B. Mannini, T. Lohr, M. Bonomi, C. Camilloni, A. De Simone, I. C. Felli, R. Pierattelli, T. P. Knowles, C. M. Dobson, M. Vendruscolo

This paper identifies a small molecule that binds and sequesters monomeric amyloid-β, inhibiting its aggregation and rescuing toxicity in a C. elegans model.

bioRxiv · Sep 16, 2020Biophysics

Structural basis for stereospecific inhibition of ASCT2 from rational design

R.-A. A. Garibsingh, E. Ndaru, A. A. Garaeva, M. Bonomi, D. J. Slotboom, C. Paulino, C. Grewer, A. Schlessinger

The paper rationally designs inhibitors for ASCT2 using computational modeling and cryo-EM, showing how stereospecific pockets can be exploited for drug discovery.

bioRxiv · May 29, 2020Biochemistry

Effects of α-tubulin acetylation on microtubule structure and stability

L. Eshun-Wilson, R. Zhang, D. Portran, M. Nachury, D. Toso, T. Lohr, M. Vendruscolo, M. Bonomi, J. Fraser, E. Nogales

This study uses cryo-EM and molecular dynamics to show that α-tubulin acetylation at K40 reduces loop disorder and may affect microtubule stability.

bioRxiv · Jan 9, 2019Biophysics