21 Publications
2024
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions
2023
Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility
 
Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility
Bauer, Magnus S.⋅Gruber, Sophia⋅Hausch, Adina⋅Melo, Marcelo C.R.⋅Gomes, Priscila S.F.C.⋅Nicolaus, Thomas⋅Milles, Lukas F.⋅Bernardi, Rafael C.⋅Gaub, Hermann E. and Lipfert, Jan
 
Fostering discoveries in the era of exascale computing: how the next-generation of supercomputers empowers computational and experimental biophysics alike. Biophysical Journal
. | Journal Article
 
Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern. Nature Nanotechnology
. | Journal Article
 
VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. Journal of Chemical Information and Modeling
Spivak, Mariano⋅Stone, John E⋅Ribeiro, João⋅Saam, Jan⋅Freddolino, Peter L⋅Bernardi, Rafael C and Tajkhorshid, Emad
. | Journal Article
2022
Bridging the gab between in vitro and in silico single-molecule force spectroscopy
 
Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections. Journal of the American Chemical Society
. | Journal Article
 
Protein structure prediction in the era of AI: challenges and limitations when applying to in-silico force spectroscopy
2020
Bacteria on steroids: the enzymatic mechanism of an NADH-dependent dehydrogenase that regulates the conversion of cortisol to androgen in the gut microbiome
Bernardi, Rafael C⋅Doden, Heidi L.⋅Melo, Marcelo C. R.⋅Devendran, Saravanan⋅Pollet, Rebecca M.⋅Mythen, Sean M.⋅Bhowmik, Shiva⋅Lesley, Scott A.⋅Cann, Isaac⋅Luthey-Schulten, Zaida⋅Koropatkin, Nicole M. and Ridlon, Jason M.
Cold Spring Harbor Laboratory
 
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
The Journal of Chemical Physics. | Journal Article
 
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
Melo, Marcelo C.R.⋅Bernardi, Rafael C⋅Fuente-Nunez, Cesar and Luthey-Shulten, Zaida
Cold Spring Harbor Laboratory
 
High force catch bond mechanism of bacterial adhesion in the human gut
Liu, Zhaowei⋅Liu, Haipei⋅Vera, Andrés M.⋅Bernardi, Rafael C.⋅Tinnefeld, Philip and Nash, Michael A.
Nature Communications, vol. 11. | Journal Article
 
High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut
Liu, Zhaowei⋅Liu, Haipei⋅Vera, Andrés M.⋅Bernardi, Rafael C.⋅Tinnefeld, Philip and Nash, Michael A.
Cold Spring Harbor Laboratory
 
Scalable molecular dynamics on CPU and GPU architectures with NAMD
Phillips, James C⋅Phillips, James C⋅Phillips, James C.⋅Hardy, David J.⋅Hardy, David J⋅Hardy, David J⋅Maia, Julio D C⋅Maia, Julio D. C.⋅Maia, Julio D C⋅Stone, John E.⋅Stone, John E⋅Stone, John E⋅Ribeiro, João V⋅Ribeiro, João V⋅Ribeiro, João V.⋅Bernardi, Rafael C⋅Bernardi, Rafael C⋅Bernardi, Rafael C.⋅Buch, Ronak⋅Buch, Ronak⋅Buch, Ronak⋅Fiorin, Giacomo⋅Fiorin, Giacomo⋅Fiorin, Giacomo⋅Hénin, Jérôme⋅Hénin, Jérôme⋅Hénin, Jérôme⋅Jiang, Wei⋅Jiang, Wei⋅Jiang, Wei⋅McGreevy, Ryan⋅McGreevy, Ryan⋅McGreevy, Ryan⋅Melo, Marcelo C R⋅Melo, Marcelo C. R.⋅Melo, Marcelo C R⋅Radak, Brian K⋅Radak, Brian K⋅Radak, Brian K.⋅Skeel, Robert D⋅Skeel, Robert D.⋅Skeel, Robert D⋅Singharoy, Abhishek⋅Singharoy, Abhishek⋅Singharoy, Abhishek⋅Wang, Yi⋅Wang, Yi⋅Wang, Yi⋅Roux, Benoît⋅Roux, Benoı̂t⋅Roux, Benoît⋅Aksimentiev, Aleksei⋅Aksimentiev, Aleksei⋅Aksimentiev, Aleksei⋅Luthey-Schulten, Zaida⋅Luthey-Schulten, Zaida⋅Luthey-Schulten, Zaida⋅Kalé, Laxmikant V⋅Kalé, Laxmikant V⋅Kalé, Laxmikant V.⋅Schulten, Klaus⋅Schulten, Klaus⋅Schulten, Klaus⋅Chipot, Christophe⋅Chipot, Christophe⋅Chipot, Christophe⋅Tajkhorshid, Emad⋅Tajkhorshid, Emad and Tajkhorshid, Emad
The Journal of Chemical Physics, vol. 153, pp. 044130. | Journal Article
 
Streptavidin/biotin: Tethering geometry defines unbinding mechanics
Science Advances. | Journal Article
2019
Direction Matters: Monovalent Streptavidin/Biotin Complex under Load
Sedlak, Steffen M.⋅Schendel, Leonard C.⋅Melo, Marcelo C. R.⋅Pippig, Diana A.⋅Luthey-Schulten, Zaida⋅Gaub, Hermann E. and Bernardi, Rafael C.
Nano Letters, vol. 19, pp. 3415–3421. | Journal Article
 
Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force Spectroscopy
Bernardi, Rafael C.⋅Durner, Ellis⋅Schoeler, Constantin⋅Malinowska, Klara H.⋅Carvalho, Bruna G.⋅Bayer, Edward A.⋅Luthey-Schulten, Zaida⋅Gaub, Hermann E. and Nash, Michael A.
Journal of the American Chemical Society, vol. 141, pp. 14752–14763. | Journal Article
2018
Molecular mechanism of extreme mechanostability in a pathogen adhesin
Milles, Lukas F.⋅Schulten, Klaus⋅Gaub, Hermann E. and Bernardi, Rafael C.
Science, vol. 359, pp. 1527–1533. | Journal Article
 
NAMD goes quantum: an integrative suite for hybrid simulations
Melo, Marcelo C R⋅Bernardi, Rafael C⋅Rudack, Till⋅Scheurer, Maximilian⋅Riplinger, Christoph⋅Phillips, James C⋅Maia, Julio D C⋅Rocha, Gerd B⋅Ribeiro, João V⋅Stone, John E⋅Neese, Frank⋅Schulten, Klaus and Luthey-Schulten, Zaida
Nature Methods, vol. 15, pp. 351–354. | Journal Article
2014
Ultrastable cellulosome-adhesion complex tightens under load
Schoeler, Constantin⋅Schoeler, Constantin⋅Malinowska, Klara H⋅Malinowska, Klara H⋅Bernardi, Rafael C⋅Bernardi, Rafael C⋅Milles, Lukas F⋅Milles, Lukas F⋅Jobst, Markus A⋅Jobst, Markus A⋅Durner, Ellis⋅Durner, Ellis⋅Ott, Wolfgang⋅Ott, Wolfgang⋅Fried, Daniel B⋅Fried, Daniel B⋅Bayer, Edward A⋅Bayer, Edward A⋅Schulten, Klaus⋅Schulten, Klaus⋅Gaub, Hermann E⋅Gaub, Hermann E⋅Nash, Michael A and Nash, Michael A
Nature Communications, vol. 5, pp. 5635, Dec 2014. | Journal Article