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 …

[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 …

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 …

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 …

Conformational cycle of a protease-containing ABC transporter in lipid nanodiscs reveals the mechanism of cargo-protein coupling

R Zhang, KL Jagessar, M Brownd, A Polasa… - Nature …, 2024 - nature.com
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 …

Asymmetric drug binding in an ATP-loaded inward-facing state of an ABC transporter

TM Thaker, S Mishra, W Zhou, M Mohan… - Nature chemical …, 2022 - nature.com
Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in
multidrug resistance, entails the ATP-powered interconversion between transporter …

Modeling of protein conformational changes with Rosetta guided by limited experimental data

D Sala, D Del Alamo, HS Mchaourab, J Meiler - Structure, 2022 - cell.com
Conformational changes are an essential component of functional cycles of many proteins,
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

Q Tang, M Sinclair, HS Hasdemir, RA Stein… - Nature …, 2023 - nature.com
Here we used cryo-electron microscopy (cryo-EM), double electron-electron resonance
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 …

Integrating Electron Paramagnetic Resonance Spectroscopy and Computational Modeling to Measure Protein Structure and Dynamics

X Bogetti, S Saxena - ChemPlusChem, 2024 - Wiley Online Library
Electron paramagnetic resonance (EPR) has become a powerful probe of conformational
heterogeneity and dynamics of biomolecules. In this Review, we discuss different …