Understanding molecular flexibility and dynamics across different structural ensembles is essential for interpreting the behavior of complex biological systems. Here, we introduce eRMSF, a fast and user-friendly Python package built with MDAKit from MDAnalysis, designed to perform ensemble-based root mean square fluctuation (RMSF) analyses. Unlike traditional approaches limited to molecular dynamics trajectories, eRMSF extends flexibility analysis to ensembles generated by different methods, such as MD simulations, BioEmu (a deep learning tool for equilibrium ensemble prediction), subsampled AlphaFold2 (AlphaFold ensemble generation), and other computational or experimental sources. By enabling RMSF calculations across heterogeneous ensembles, eRMSF provides a unified framework to evaluate residue or atomic fluctuations in both simulated and predicted structures. Users can easily customize atom, residue, or region selections, tailoring analyses to specific research questions. This approach delivers high-resolution insights into localized motions, complements global stability assessments, and reveals dynamic regions often overlooked by single-method analyses. The repository for eRMSF is available at https://github.com/pablo-arantes/ermsfkit.

ParametrizANI - Fast, Accurate and Free Dihedral Parametrization in the Cloud with TorchANI - palermolab/ParametrizANI

In molecular studies, the accurate parametrization of small molecules stands as an essential yet growing demand. Addressing this, we introduce ParametrizANI, a tool crafted explicitly for establishing...

ALT: a robot says hey guys in a purple light

Brazil’s attorney general charged the former president Jair Bolsonaro with trying to overturn the 2022 elections.

Abstract. CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were deve