Rafael C Bernardi
Rafael C Bernardi
Assistant Professor - Department of Physics at Auburn University
Verified email at auburn.edu - Homepage
Title
Cited by
Cited by
Year
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
3722015
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
2892015
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
862014
Molecular mechanism of extreme mechanostability in a pathogen adhesin
LF Milles, K Schulten, HE Gaub, RC Bernardi
Science 359 (6383), 1527-1533, 2018
752018
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
672016
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
572018
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
562016
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
502015
Molecular dynamics study of enhanced Man5B enzymatic activity
RC Bernardi, I Cann, K Schulten
Biotechnology for Biofuels 7 (1), 83, 2014
342014
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
332020
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
312016
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
292017
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
242019
Molecular dynamics study of biomembrane/local anesthetics interactions
RC Bernardi, DEB Gomes, R Gobato, CA Taft, AT Ota, PG Pascutti
Molecular Physics 107 (14), 1437-1443, 2009
212009
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
202018
Hybrid QM/MM molecular dynamics study of benzocaine in a membrane environment: how does a quantum mechanical treatment of both anesthetic and lipids affect their interaction
RC Bernardi, PG Pascutti
Journal of Chemical Theory and Computation 8 (7), 2197-2203, 2012
192012
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
182019
The structural dynamics of the flavivirus fusion peptide–membrane interaction
YS Mendes, NS Alves, TLF Souza, IP Sousa Jr, ML Bianconi, RC Bernardi, ...
PLoS One 7 (10), e47596, 2012
172012
Streptavidin/biotin: Tethering geometry defines unbinding mechanics
SM Sedlak, LC Schendel, HE Gaub, RC Bernardi
Science Advances 6 (13), eaay5999, 2020
142020
GSAFold: a new application of GSA to protein structure prediction
MCR Melo, RC Bernardi, TVA Fernandes, PG Pascutti
Proteins: Structure, Function, and Bioinformatics 80 (9), 2305-2310, 2012
122012
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