CHARMM at 45: Enhancements in accessibility, functionality, and speed
W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …
computational biochemistry and biophysics. Commensurate with the developments in …
[HTML][HTML] Hybrid methods for combined experimental and computational determination of protein structure
JT Seffernick, S Lindert - The Journal of chemical physics, 2020 - pubs.aip.org
Knowledge of protein structure is paramount to the understanding of biological function,
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …
developing new therapeutics, and making detailed mechanistic hypotheses. Therefore …
chiLife: An open-source Python package for in silico spin labeling and integrative protein modeling
MH Tessmer, S Stoll - PLOS Computational Biology, 2023 - journals.plos.org
Here we introduce chiLife, a Python package for site-directed spin label (SDSL) modeling for
electron paramagnetic resonance (EPR) spectroscopy, in particular double electron …
electron paramagnetic resonance (EPR) spectroscopy, in particular double electron …
pyCHARMM: embedding CHARMM functionality in a python framework
J Buckner, X Liu, A Chakravorty, Y Wu… - Journal of chemical …, 2023 - ACS Publications
CHARMM is rich in methodology and functionality as one of the first programs addressing
problems of molecular dynamics and modeling of biological macromolecules and their …
problems of molecular dynamics and modeling of biological macromolecules and their …
Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling
Protease-containing ABC transporters (PCATs) couple the energy of ATP hydrolysis to the
processing and export of diverse cargo proteins across cell membranes to mediate …
processing and export of diverse cargo proteins across cell membranes to mediate …
Asymmetric drug binding in an ATP-loaded inward-facing state of an ABC transporter
Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in
multidrug resistance, entails the ATP-powered interconversion between transporter …
multidrug resistance, entails the ATP-powered interconversion between transporter …
Modeling of protein conformational changes with Rosetta guided by limited experimental data
Conformational changes are an essential component of functional cycles of many proteins,
but their characterization often requires an integrative structural biology approach. Here, we …
but their characterization often requires an integrative structural biology approach. Here, we …
Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter
Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance
spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and …
spectroscopy (DEER), and molecular dynamics (MD) simulations, to capture and …
Integration of nanometer-range label-to-label distances and their distributions into modelling approaches
G Jeschke - Biomolecules, 2022 - mdpi.com
Labelling techniques such as electron paramagnetic resonance spectroscopy and single-
molecule fluorescence resonance energy transfer, allow access to distances in the range of …
molecule fluorescence resonance energy transfer, allow access to distances in the range of …
Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational
heterogeneity and dynamics of biomolecules. In this Review, we discuss different …
heterogeneity and dynamics of biomolecules. In this Review, we discuss different …