BILBY-MD shows static scaffolding fails dynamical fidelity
Original title: Static Recovery Is Not Dynamic Stability: Dynamics-Aware Benchmarking of Protein Motif Scaffolding
BILBY-MD finds only 8 of 55 static designs satisfy molecular dynamics criteria for motif scaffolding.
Protein motif scaffolding benchmarks use static refolding but ignore conformational ensembles. BILBY-PRO derives 220 conserved motifs from PROSITE. BILBY-MD evaluates six models, with only 31 of 55 pairs meeting MD-supported fidelity for motif drift and contacts.
- BILBY-PRO covers 220 cases from 174 PROSITE entries
- ESM3 yields more unique scaffolds
- RFDiffusion and Proteina solve more targets
- Static success does not ensure full scaffold dynamics
From the original article
1 min read at huggingface.co
Protein motif scaffolding benchmarks assess whether generative models can build scaffolds around functionally important residues. Their conclusions depend on which motifs are tested and which criteria define success. Existing benchmarks typically use small hand-curated motif sets and static refolding criteria, but protein function often depends on conformational ensembles and transitions.
By Emile de Bruyn, Moritz Schäffler, Jannik Schneider · huggingface.co
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