31 Publications (Page 1 of 2)
2026
Mapping of dynamic allostery within p38 alpha kinase via network analyses and NMR spectroscopy
 
Mapping of dynamic allostery within p38 alpha kinase via network analyses and NMR spectroscopy. Nature Communications
. | Journal Article
2025
AI Uncovers the Rapid Activation of Catch-Bonds under Force. Journal of Chemical Theory and Computation
. | Journal Article
 
Atomistic Insights into gp82 Binding: A Microsecond, Million-Atom Exploration of Trypanosoma cruzi Host-Cell Invasion. Biochemistry
. | Journal Article
 
Impact of Structural Relaxation on Protein–Protein Docking in Large Macromolecular Complexes. Applied Biosciences
. | Journal Article
 
Probing SARS-CoV-2 membrane binding peptide via single-molecule AFM-based force spectroscopy. Nature Communications
. | Journal Article
 
Ultra-Strong Staphylococcus aureus Adhesion to Human Skin: Calcium as a Key Regulator of Non-Covalent Interactions. Science Advances
. | Journal Article
2024
Engineering the Mechanical Stability of a Therapeutic Affibody/PD-L1 Complex by Anchor Point Selection
 
Engineering the Mechanical Stability of a Therapeutic Complex between Affibody and Programmed Death-Ligand 1 by Anchor Point Selection. ACS Nano
. | Journal Article
 
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions
 
Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions. Journal of the American Chemical Society
. | Journal Article
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
Melo, Marcelo C.R.
. | 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