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Hassan Nadeem

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#protein folding Open access Oct 2026

β-Hairpin Fold Peptide Brush Polymers

Peptide-brush polymers prepared via graft-through polymerization of peptide-based olefinic monomers form Protein-Like Polymers (PLPs) with demonstrated utility as chemical biology tools for modulating intracellular protein–protein interactions and are in development as a emerging class of therapeutic. This favorable bi...

Julia Oktawiec, Hassan Nadeem, Omar M. Ebrahim et al. · 0 citations
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

Mapping the sequence preference of the generalist class II lanthipeptide synthetase ProcM by mRNA display

This study uses the ultrahigh-throughput mRNA display technique to map the sequence compatibility of ProcM across a focused library and provides a high-throughput view of ProcM reactivity and highlights differences with previous high-throughput studies on substrate selectivity of RiPP modification enzymes.

Ouyang Yao, Hassan Nadeem, Y. Goto et al. · 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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