Author

R. C. Bernardi

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· 7 Microbiology· 1

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 5 Research Focus:host-pathogen & immune response· 4 Organism:human· 4 Assay:proteomics· 4 Approach:statistical model· 4 Approach:deep learning· 3 Approach:experimental assay· 3 Organism:bacteria (other)· 1

Frequent Co-Authors

M. C. R. Melo· 4 shared D. E. B. Gomes· 3 shared A. Hausch· 2 shared H. E. Gaub· 2 shared J. Lipfert· 2 shared L. F. Milles· 2 shared M. A. Nash· 2 shared M. S. Bauer· 2 shared

Activity by Year

2020-2024 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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4 shared papersBiophysics

M. C. R. Melo

Mutual co-authors in cluster

Author profile →

8 papers

Recent·Most cited

Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions

D. E. B. Gomes, B. Yang, R. Vanella, M. A. Nash, R. C. Bernardi

The paper develops an integrated method combining dynamic network analysis with AI to predict epitopes in PD-L1:Affibody interactions, showing the perpendicular binding mode is more stable.

bioRxiv · Feb 8, 2024Biophysics

Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility

M. S. Bauer, S. Gruber, A. Hausch, M. C. R. Melo, P. S. F. C. Gomes, T. Nicolaus, L. F. Milles, R. C. Bernardi, H. E. Gaub, J. Lipfert

This study examines how mutations in SARS-CoV-2 variants affect the force-stability of the SARS-CoV-2:ACE2 interface and virus transmissibility.

bioRxiv · Jan 6, 2023 · PreprintBiophysics

May the force be with you: the role of hyper-mechanostability of the bone sialoprotein binding protein during early stages of Staphylococci infections

P. S. Gomes, M. Forrester, M. Pace, D. E. B. Gomes, R. C. Bernardi

The paper investigates the mechanostability of the Bbp:Fg complex using SMFS and SMD simulations, finding Bbp to be highly mechanostable with rupture forces exceeding 2 nN.

bioRxiv · Dec 9, 2022Biophysics

Bridging the gap between in vitro and in silico single-molecule force spectroscopy

D. E. B. Gomes, M. C. R. Melo, P. S. F. C. Gomes, R. C. Bernardi

The paper bridges the gap between in vitro and in silico single-molecule force spectroscopy by combining coarse-grained and all-atom SMD simulations with DHS theory.

bioRxiv · Jul 14, 2022 · PreprintBiophysics

A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions

M. S. Bauer, S. Gruber, A. Hausch, L. F. Milles, T. Nicolaus, L. C. Schendel, P. Lopez Navajas, E. Procko, D. Lietha, R. C. Bernardi, H. E. Gaub, J. Lipfert

This paper introduces a tethered ligand assay to study SARS-CoV-2:ACE2 interactions under mechanical force, showing higher stability and lower dissociation rates compared to SARS-CoV-1.

bioRxiv · Aug 8, 2021 · PreprintBiophysics

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories

M. C. R. Melo, R. C. Bernardi, C. de la Fuente-Nunez, Z. Luthey-Shulten

This paper introduces an enhanced dynamical network analysis method for identifying allosteric communications in molecular dynamics trajectories, applied to large biomolecular systems.

The Journal of Chemical Physics · Oct 1, 2020Peer-reviewedBiophysics

Gut bacteria convert cortisol into a distinct hostsignalling molecule

M. Freiberg, T. Wang, R. S. d. L. Rosa, A. Osswald, M. C. R. Melo, D. G. Stouffer, P. S. Buobu, C. Welsh, L. Yang, A. M. Abdel-Hamid, H. L. Doden, S. Devendran, R. M. Pollet, S. Goldberg, L. Ray, , J. M. Ridlon

The paper shows gut bacteria convert cortisol into 20-dihydrocortisol, a distinct host signalling molecule that reprograms colonic transcription and activates inflammatory pathways via NR4A3.

bioRxiv · Jun 12, 2020 · PreprintMicrobiology

High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut

Z. Liu, H. Liu, A. M. Vera, R. C. Bernardi, P. Tinnefeld, M. A. Nash

The paper identifies a catch bond mechanism in a bacterial adhesion complex that resists high shear forces in the human gut.

bioRxiv · Jan 21, 2020Biophysics