Markov state models: From an art to a science
Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
such as molecular dynamics (MD) simulations, that have gained widespread use over the …
Crossroads of antibiotic resistance and biosynthesis
TA Wencewicz - Journal of molecular biology, 2019 - Elsevier
The biosynthesis of antibiotics and self-protection mechanisms employed by antibiotic
producers are an integral part of the growing antibiotic resistance threat. The origins of …
producers are an integral part of the growing antibiotic resistance threat. The origins of …
[HTML][HTML] The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA
Abstract The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein
critical for viral genome packaging, yet the molecular details that underlie this process are …
critical for viral genome packaging, yet the molecular details that underlie this process are …
SARS-CoV-2 simulations go exascale to capture spike opening and reveal cryptic pockets across the proteome
MI Zimmerman, G Bowman - Biophysical Journal, 2021 - cell.com
The SARS-CoV-2/COVID-19 pandemic continues to threaten global health and
socioeconomic stability. Experiments have revealed snapshots of many viral components …
socioeconomic stability. Experiments have revealed snapshots of many viral components …
Discovery of novel gain-of-function mutations guided by structure-based deep learning
Despite the promise of deep learning accelerated protein engineering, examples of such
improved proteins are scarce. Here we report that a 3D convolutional neural network trained …
improved proteins are scarce. Here we report that a 3D convolutional neural network trained …
Folding@ home: Achievements from over 20 years of citizen science herald the exascale era
Simulations of biomolecules have enormous potential to inform our understanding of biology
but require extremely demanding calculations. For over 20 years, the Folding@ home …
but require extremely demanding calculations. For over 20 years, the Folding@ home …
Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets
Understanding the structural determinants of a protein's biochemical properties, such as
activity and stability, is a major challenge in biology and medicine. Comparing computer …
activity and stability, is a major challenge in biology and medicine. Comparing computer …
SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential
Coronaviruses have caused multiple epidemics in the past two decades, in addition to the
current COVID-19 pandemic that is severely damaging global health and the economy …
current COVID-19 pandemic that is severely damaging global health and the economy …
The interplay of electrostatics and chemical positioning in the evolution of antibiotic resistance in TEM β-lactamases
The interplay of enzyme active site electrostatics and chemical positioning is important for
understanding the origin (s) of enzyme catalysis and the design of novel catalysts. We …
understanding the origin (s) of enzyme catalysis and the design of novel catalysts. We …
Structure–function correlates of fibrinogen binding by Acinetobacter adhesins critical in catheter-associated urinary tract infections
KO Tamadonfar, G Di Venanzio… - Proceedings of the …, 2023 - National Acad Sciences
Multidrug-resistant Acinetobacter baumannii infections are an urgent clinical problem and
can cause difficult-to-treat nosocomial infections. During such infections, like catheter …
can cause difficult-to-treat nosocomial infections. During such infections, like catheter …