26 Publications (Page 1 of 2)
2025
Atomistic Insights into gp82 Binding: A Microsecond, Million-Atom Exploration of Trypanosoma cruzi Host-Cell Invasion. Biochemistry
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Probing SARS-CoV-2 membrane binding peptide via single-molecule AFM-based force spectroscopy. Nature Communications
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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
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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
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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 TransmissibilityBauer, 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
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Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern. Nature Nanotechnology
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VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations. Journal of Chemical Information and ModelingSpivak, Mariano⋅Stone, John E⋅Ribeiro, João⋅Saam, Jan⋅Freddolino, Peter L⋅Bernardi, Rafael C and Tajkhorshid, Emad.
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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
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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 microbiomeBernardi, 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 trajectoriesMelo, Marcelo C.R.⋅Bernardi, Rafael C⋅Fuente-Nunez, Cesar and Luthey-Shulten, ZaidaCold Spring Harbor Laboratory
High force catch bond mechanism of bacterial adhesion in the human gutLiu, Zhaowei⋅Liu, Haipei⋅Vera, Andrés M.⋅Bernardi, Rafael C.⋅Tinnefeld, Philip and Nash, Michael A.Nature Communications, vol. 11.
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High Force Catch Bond Mechanism of Bacterial Adhesion in the Human GutLiu, 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 NAMDPhillips, 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, EmadThe Journal of Chemical Physics, vol. 153, pp. 044130.
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Streptavidin/biotin: Tethering geometry defines unbinding mechanics
Science Advances. | Journal Article
2019
Direction Matters: Monovalent Streptavidin/Biotin Complex under LoadSedlak, 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.
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Mechanisms of Nanonewton Mechanostability in a Protein Complex Revealed by Molecular Dynamics Simulations and Single-Molecule Force SpectroscopyBernardi, 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.
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2018
Molecular mechanism of extreme mechanostability in a pathogen adhesinMilles, Lukas F.⋅Schulten, Klaus⋅Gaub, Hermann E. and Bernardi, Rafael C.Science, vol. 359, pp. 1527–1533.
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NAMD goes quantum: an integrative suite for hybrid simulationsMelo, 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, ZaidaNature Methods, vol. 15, pp. 351–354.
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