11 Publications
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 CDoden, Heidi L.Melo, Marcelo C. R.Devendran, SaravananPollet, Rebecca M.Mythen, Sean M.Bhowmik, ShivaLesley, Scott A.Cann, IsaacLuthey-Schulten, ZaidaKoropatkin, 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
Melo, Marcelo C.R.Bernardi, Rafael CFuente-Nunez, Cesar and Luthey-Shulten, Zaida
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
 
High force catch bond mechanism of bacterial adhesion in the human gut
Liu, ZhaoweiLiu, HaipeiVera, 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, ZhaoweiLiu, HaipeiVera, 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 CPhillips, James CHardy, David JHardy, David J.Hardy, David JMaia, Julio D CMaia, Julio D CMaia, Julio D. C.Stone, John EStone, John E.Stone, John ERibeiro, João VRibeiro, João VRibeiro, João V.Bernardi, Rafael CBernardi, Rafael C.Bernardi, Rafael CBuch, RonakBuch, RonakBuch, RonakFiorin, GiacomoFiorin, GiacomoFiorin, GiacomoHénin, JérômeHénin, JérômeHénin, JérômeJiang, WeiJiang, WeiJiang, WeiMcGreevy, RyanMcGreevy, RyanMcGreevy, RyanMelo, Marcelo C RMelo, Marcelo C. R.Melo, Marcelo C RRadak, Brian K.Radak, Brian KRadak, Brian KSkeel, Robert DSkeel, Robert D.Skeel, Robert DSingharoy, AbhishekSingharoy, AbhishekSingharoy, AbhishekWang, YiWang, YiWang, YiRoux, BenoîtRoux, BenoîtRoux, Benoı̂tAksimentiev, AlekseiAksimentiev, AlekseiAksimentiev, AlekseiLuthey-Schulten, ZaidaLuthey-Schulten, ZaidaLuthey-Schulten, ZaidaKalé, Laxmikant VKalé, Laxmikant V.Kalé, Laxmikant VSchulten, KlausSchulten, KlausSchulten, KlausChipot, ChristopheChipot, ChristopheChipot, ChristopheTajkhorshid, EmadTajkhorshid, 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, ZaidaGaub, 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, EllisSchoeler, ConstantinMalinowska, Klara H.Carvalho, Bruna G.Bayer, Edward A.Luthey-Schulten, ZaidaGaub, 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, KlausGaub, 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 RBernardi, Rafael CRudack, TillScheurer, MaximilianRiplinger, ChristophPhillips, James CMaia, Julio D CRocha, Gerd BRibeiro, João VStone, John ENeese, FrankSchulten, Klaus and Luthey-Schulten, Zaida
Nature Methods, vol. 15, pp. 351–354. | Journal Article