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Protein Design

Created Apr 10, 2026Modified Apr 20, 2026

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General

2 items with this tag.

Apr 21, 2026
Multimodal sequence-structure guidance outperforms unimodal guidance in cases where both need to be designed
Apr 21, 2026
Search algorithms are more important than language model choice for model-guided protein engineering and design
- protein-design

Design

19 items with this tag.

Apr 21, 2026
Inference-time scaling of de novo designed proteins is more effective for harder targets
Apr 21, 2026
Backbone diffusion works best on small protein sizes
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Diffusion outperforms hallucination when using AF3-generation protein structure prediction methods
Apr 21, 2026
Diffusion-based protein design methods undersample structural diversity in specific topologies
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Guided sequence-only diffusion outperforms autoregressive fine-tuned PLMs on designing high-fitness sequences
Apr 21, 2026
Hallucination outperforms diffusion on protein refolding accuracy, particularly among larger proteins
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
No one-size-fits-all best approach to motif scaffolding protein design
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Partial diffusion of protein structures reduces structural complexity
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Partial structure diffusion can make de novo backbones more designable
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Protein backbone diffusion models undersample loop-rich and alpha-beta domains and functional motifs
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Protein backbones designed by diffusion, but not by language models, have more secondary structure
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Protein backbones designed using diffusion, but not sequence-based models, have fewer beta sheets
Apr 21, 2026
Protein language models can be steered to design proteins with specific properties
- protein-design/design
Apr 21, 2026
Proteins designed by diffusion are more compact than those designed by hallucination
- diffusion-models/protein-design
- protein-design/design
Apr 21, 2026
Stronger diffusion guidance reduces diversity of generated outputs
Apr 21, 2026
Subquadratic scaling for protein backbone diffusion
- diffusion-models/implementation
- protein-design/design
Apr 21, 2026
Accurate fitness landscapes are unnecessary for productively engineering enzymes or proteins
- protein-design/design
Apr 21, 2026
De novo designed proteins (from language models) and naturally occurring proteins borrow heavily from other functionally similar sequences
- protein-design/design
Apr 21, 2026
Individual mutations insufficient to lock fusion proteins in one state
- protein-design/design

Enzyme design

5 items with this tag.

Apr 21, 2026
Beneficial mutations of enzymes far from active site improve substrate binding and product release
- protein-design/enzyme-design
Apr 21, 2026
Epistasis in enzymes can arise from changes in the rate-limiting step of the catalytic cycle
- epistasis
- protein-design/enzyme-design
Apr 21, 2026
PLMs generate more divergent functional proteins than Potts models
- protein-design/enzyme-design
Apr 21, 2026
MD simulations can distinguish enzyme design candidates for catalytically competent substates
- protein-design/enzyme-design
Apr 21, 2026
Rigidification of active site residues accelerates enzyme activity
- protein-design/enzyme-design

Training

2 items with this tag.

Apr 21, 2026
Training backbone diffusion models on synthetic data improves designability
- diffusion-models/training
- protein-design/training
Apr 21, 2026
Training inverse folding and diffusion models exclusively on predicted protein structures worsens performance due to how locally perfect they are
- diffusion-models/training
- protein-design/training

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