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J. Velasquez

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Open access Aug 2026

Cross-taxon Coarse-Grained IDP Simulations Enable Architecture-Independent Generalization

BENDER, a dataset of 11,533 IDP sequences spanning 13 taxonomic groups, each simulated under CALVADOS-2 molecular dynamics and annotated with ensemble-level geometric and novel contact-network properties, suggests that hub topology in disordered protein contact networks is a conserved physical feature of sequence-encod...

J. Velasquez, Taseef Rahman · 0 citations
Open access Aug 2026

BENDER: A Cross-taxon IDP Simulation Database Reveals Conserved Sequence-Ensemble Laws Across the Tree of Life

Intrinsically disordered proteins and regions are found across all kingdoms of life, yet the computational characterisation of their conformational ensembles has remained almost entirely confined to the human proteome. Whether the physics-based force fields developed on eukaryotic sequences remain reliable for taxonomi...

J. Velasquez, Taseef Rahman · 0 citations

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