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D. Kleiman

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Open access Aug 2026

AdaptivePy: a unified Python framework for adaptive sampling in molecular dynamics

AdaptivePy is presented, a compact and extensible Python framework that implements nine seed-selection policies behind a single configuration-driven interface, spanning simple population-based baselines, several established machine-learning and geometry-based methods, and two ensemble or meta sampling policies introduc...

Hassan Nadeem, D. Kleiman, Diwakar Shukla · 0 citations
Open access Aug 2026

Pi-Ensemble: Sequence-guided generation of interpolated protein conformational ensembles

Pi-Ensemble (Predicting Interpolated Ensemble), a sequence-guided framework for generating protein conformational ensembles interpolating between two structural anchor states, provides an extensible framework for studying protein flexibility, guiding adaptive sampling, and accelerating mechanistic investigations of pro...

Hassan Nadeem, D. Kleiman, Yu-Ming Zhou et al. · 0 citations

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