Rafael C Bernardi

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 26

Top Venues

bioRxiv : the preprint server for biology

Journal of the American Chemical Society

Proceedings of the National Academy of Sciences of the United States of America

The Journal of chemical physics

University of Illinois at Urbana-Champaign

Universidade Federal do Rio de Janeiro (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Illinois at Urbana-Champaign

United States

Associate Researcher :: Beckman Institute

Instituto Nacional de Metrologia Normalização e Qualidade Industrial

Brazil

Pesquisador

Education History

Universidade Federal do Rio de Janeiro

Brazil

PHD :: Instituto de Biofísica Carlos Chagas Filho

Centro Brasileiro de Pesquisas Físicas

Brazil

MSC

Universidade Estadual de Londrina

Brazil

BSC :: Departamento de Física

Publications

Byeongseon Yang, Diego E B Gomes, Zhaowei Liu, Mariana Sá Santos, Jiajun Li, Rafael C Bernardi, Michael A Nash
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. bioRxiv : the preprint server for biology (2024)
Byeongseon Yang, Diego E B Gomes, Zhaowei Liu, Mariana Sá Santos, Jiajun Li, Rafael C Bernardi, Michael A Nash
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. bioRxiv : the preprint server for biology (2024)
Byeongseon Yang, Diego E B Gomes, Zhaowei Liu, Mariana Sá Santos, Jiajun Li, Rafael C Bernardi, Michael A Nash
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. bioRxiv : the preprint server for biology (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. Journal of the American Chemical Society 146 (34) (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. bioRxiv : the preprint server for biology (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. bioRxiv : the preprint server for biology (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. bioRxiv : the preprint server for biology (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. Journal of the American Chemical Society (2024)
Byeongseon Yang, Diego E B Gomes, Zhaowei Liu, Mariana Sá Santos, Jiajun Li, Rafael C Bernardi, Michael A Nash
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. bioRxiv : the preprint server for biology (2024)
Diego E B Gomes, Byeongseon Yang, Rosario Vanella, Michael A Nash, Rafael C Bernardi
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. Journal of the American Chemical Society (2024)
Byeongseon Yang, Diego E B Gomes, Zhaowei Liu, Mariana Sá Santos, Jiajun Li, Rafael C Bernardi, Michael A Nash
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection. bioRxiv : the preprint server for biology (2024)
Rita Dos Santos Natividade, Melanie Koehler, Priscila da Silva Figueiredo Celestino Gomes, Joshua D Simpson, Sydni Caet Smith, Diego E B Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S Dermody, Rafael C Bernardi, Kristen M Ogden, David Alsteens
Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proceedings of the National Academy of Sciences of the United States of America 120 (21) (2023)
Magnus Sebastian Bauer, Sophia Gruber, Adina Hausch, Marcelo Cardoso Dos Reis Melo, Priscila da Silva Figueiredo Celestino Gomes, Thomas Nicolaus, Lukas F Milles, Hermann E Gaub, Rafael C Bernardi, Jan Lipfert
Single-molecule force stability of the SARS-CoV-2-ACE2 interface in variants-of-concern. Nature nanotechnology (2023)
Mariano Spivak, John E Stone, João Ribeiro, Jan Saam, Peter L Freddolino, Rafael C Bernardi, Emad Tajkhorshid
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. Journal of chemical information and modeling (2023)
Rita Dos Santos Natividade, Melanie Koehler, Priscila da Silva Figueiredo Celestino Gomes, Joshua D Simpson, Sydni Caet Smith, Diego E B Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S Dermody, Rafael C Bernardi, Kristen M Ogden, David Alsteens
Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proceedings of the National Academy of Sciences of the United States of America 120 (21) (2023)
Rita Dos Santos Natividade, Melanie Koehler, Priscila da Silva Figueiredo Celestino Gomes, Joshua D Simpson, Sydni Caet Smith, Diego E B Gomes, Juliette de Lhoneux, Jinsung Yang, Ankita Ray, Terence S Dermody, Rafael C Bernardi, Kristen M Ogden, David Alsteens
Deciphering molecular mechanisms stabilizing the reovirus-binding complex. Proceedings of the National Academy of Sciences of the United States of America 120 (21) (2023)
Marcelo Cardoso Dos Reis Melo, Diego E B Gomes, Rafael C Bernardi
Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. Journal of the American Chemical Society (2022)
Magnus Sebastian Bauer, Sophia Gruber, Adina Hausch, Priscila da Silva Figueiredo Celestino Gomes, Lukas F Milles, Thomas Nicolaus, Leonard C Schendel, Pilar López Navajas, Erik Procko, Daniel Lietha, Marcelo Cardoso Dos Reis Melo, Rafael C Bernardi, Hermann Eduard Gaub, Jan Lipfert
A tethered ligand assay to probe SARS-CoV-2:ACE2 interactions. Proceedings of the National Academy of Sciences of the United States of America 119 (14) (2022)
Marcelo Cardoso Dos Reis Melo, Rafael C Bernardi, Cesar de la Fuente-Nunez, Zaida Luthey-Schulten
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories. The Journal of chemical physics 153 (13) (2021)
Zhaowei Liu, Haipei Liu, Andrés Manuel Vera, Rafael C Bernardi, Philip Tinnefeld, Michael A Nash
High force catch bond mechanism of bacterial adhesion in the human gut. Nature communications 11 (1) (2020)
James C Phillips, David J Hardy, Julio D C Maia, John E Stone, João V Ribeiro, Rafael C Bernardi, Ronak Buch, Giacomo Fiorin, Jérôme Hénin, Wei Jiang, Ryan McGreevy, Marcelo Cardoso Dos Reis Melo, Brian K Radak, Robert D Skeel, Abhishek Singharoy, Yi Wang, Benoı T Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V Kalé, Klaus Schulten, Christophe J Chipot, Emad Tajkhorshid
Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of chemical physics 153 (4) (2020)
Steffen M Sedlak, Leonard C Schendel, Hermann Eduard Gaub, Rafael C Bernardi
Streptavidin/biotin: Tethering geometry defines unbinding mechanics. Science advances 6 (13) (2020)
Rafael C Bernardi, Ellis Durner, Constantin Schoeler, Klara H Malinowska, Bruna G Carvalho, Edward A Bayer, Zaida Luthey-Schulten, Hermann Eduard Gaub, Michael A Nash
Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy. Journal of the American Chemical Society 141 (37) (2019)
Steffen M Sedlak, Leonard C Schendel, Marcelo Cardoso Dos Reis Melo, Diana A Pippig, Zaida Luthey-Schulten, Hermann Eduard Gaub, Rafael C Bernardi
Direction Matters: Monovalent Streptavidin/Biotin Complex under Load. Nano letters 19 (6) (2018)
Marcelo Cardoso Dos Reis Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd Bruno Rocha, João V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, Zaida Luthey-Schulten
NAMD goes quantum: an integrative suite for hybrid simulations. Nature methods 15 (5) (2018)
Lukas F Milles, Klaus Schulten, Hermann Eduard Gaub, Rafael C Bernardi
Molecular mechanism of extreme mechanostability in a pathogen adhesin. Science (New York, N.Y.) 359 (6383) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Rafael C Bernardi