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Bridging the Gap: AI, MD, and De Novo Design
AI
Molecular Dynamics
De Novo Design
The Hybrid Approach
Combining the speed of AI with the physics of MD and the precision of local quality estimation.
Machine Learning
Initial structure generation
Molecular Dynamics
Conformational sampling
Quality Estimation
Adaptive restraints
Figure: ReFOLD3 refining SARS-CoV-2 viral protein structures
Why Local Quality Matters
Protein motion isn't uniform. Stable cores need tight restraints. Flexible loops need freedom. Local quality scores let us distinguish between them, refining uncertain regions while preserving well-predicted ones.
De Novo Design
Model novel folds where evolutionary information is absent
Mutant Modelling
Capture subtle structural changes that determine stability