Ikuti
Rafael C Bernardi
Rafael C Bernardi
Associate Professor - Department of Physics at Auburn University
Email yang diverifikasi di auburn.edu - Beranda
Judul
Dikutip oleh
Dikutip oleh
Tahun
Scalable molecular dynamics on CPU and GPU architectures with NAMD
JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ...
The Journal of Chemical Physics 153 (4), 044130, 2020
24352020
Enhanced sampling techniques in molecular dynamics simulations of biological systems
RC Bernardi, MCR Melo, K Schulten
Biochimica et Biophysica Acta (BBA)-General Subjects 1850 (5), 872-877, 2015
8252015
Molecular dynamics simulations of large macromolecular complexes
JR Perilla, BC Goh, CK Cassidy, B Liu, RC Bernardi, T Rudack, H Yu, ...
Current Opinion in Structural Biology 31, 64-74, 2015
4752015
NAMD goes quantum: an integrative suite for hybrid simulations
MCR Melo, RC Bernardi, T Rudack, M Scheurer, C Riplinger, JC Phillips, ...
Nature Methods 15 (5), 351, 2018
2252018
QwikMD—integrative molecular dynamics toolkit for novices and experts
JV Ribeiro, RC Bernardi, T Rudack, JE Stone, JC Phillips, PL Freddolino, ...
Scientific Reports 6 (1), 1-14, 2016
2132016
Molecular mechanism of extreme mechanostability in a pathogen adhesin
LF Milles, K Schulten, HE Gaub, RC Bernardi
Science 359 (6383), 1527-1533, 2018
2122018
Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics trajectories
MCR Melo, RC Bernardi, C De La Fuente-Nunez, Z Luthey-Schulten
The Journal of Chemical Physics 153 (13), 2020
1152020
PyContact: Rapid, customizable, and visual analysis of noncovalent interactions in MD simulations
M Scheurer, P Rodenkirch, M Siggel, RC Bernardi, K Schulten, ...
Biophysical Journal 114 (3), 577-583, 2018
1132018
Ultrastable cellulosome-adhesion complex tightens under load
C Schoeler, KH Malinowska, RC Bernardi, LF Milles, MA Jobst, E Durner, ...
Nature Communications 5 (1), 1-8, 2014
1092014
Mapping mechanical force propagation through biomolecular complexes
C Schoeler, RC Bernardi, KH Malinowska, E Durner, W Ott, EA Bayer, ...
Nano Letters 15 (11), 7370-7376, 2015
922015
Streptavidin/biotin: Tethering geometry defines unbinding mechanics
SM Sedlak, LC Schendel, HE Gaub, RC Bernardi
Science advances 6 (13), eaay5999, 2020
802020
Computational methodologies for real-space structural refinement of large macromolecular complexes
BC Goh, JA Hadden, RC Bernardi, A Singharoy, R McGreevy, T Rudack, ...
Annual Review of Biophysics 45, 253-278, 2016
802016
Mechanisms of nanonewton mechanostability in a protein complex revealed by molecular dynamics simulations and single-molecule force spectroscopy
RC Bernardi, E Durner, C Schoeler, KH Malinowska, BG Carvalho, ...
Journal of the American Chemical Society 141 (37), 14752-14763, 2019
722019
Cellulose degradation in the human gut: Ruminococcus champanellensis expands the cellulosome paradigm
I Cann, RC Bernardi, RI Mackie
Environmental Microbiology 18 (2), 307-310, 2016
632016
Direction Matters: Monovalent Streptavidin/Biotin Complex under Load
SM Sedlak, LC Schendel, MCR Melo, DA Pippig, Z Luthey-Schulten, ...
Nano Letters 19 (6), 3415-3421, 2019
622019
High Force Catch Bond Mechanism of Bacterial Adhesion in the Human Gut
Z Liu, H Liu, AM Vera, RC Bernardi, P Tinnefeld, MA Nash
Nature Communications 11, 4321, 2020
602020
Combining in Vitro and in Silico Single-Molecule Force Spectroscopy to Characterize and Tune Cellulosomal Scaffoldin Mechanics
T Verdorfer, RC Bernardi, A Meinhold, W Ott, Z Luthey-Schulten, MA Nash, ...
Journal of the American Chemical Society 139 (49), 17841-17852, 2017
552017
A tethered ligand assay to probe SARS-CoV-2: ACE2 interactions
MS Bauer, S Gruber, A Hausch, LF Milles, T Nicolaus, LC Schendel, ...
Proceedings of the National Academy of Sciences 119 (14), e2114397119, 2022
542022
Molecular dynamics study of enhanced Man5B enzymatic activity
RC Bernardi, I Cann, K Schulten
Biotechnology for Biofuels 7 (1), 83, 2014
462014
VMD as a platform for interactive small molecule preparation and visualization in quantum and classical simulations
M Spivak, JE Stone, J Ribeiro, J Saam, L Freddolino, RC Bernardi, ...
Journal of chemical information and modeling 63 (15), 4664-4678, 2023
382023
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