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Stability and expression

Stability and expression

Created Sep 26, 2026Modified Sep 07, 2026

Predicting stability, folding cooperativity, expression, solubility, and related physical developability properties.

40 items with this tag.

Sep 07, 2026
ESMFold pLDDT weakly correlates with intra-family differences in stability and experimental success, but not differences in cooperativity
Aug 25, 2026
Zero-shot protein stability prediction using inverse folding models can be improved by subtracting predictions from residue in isolation
- prediction/stability-expression
- design/inverse-folding
Aug 19, 2026
Raw folding-model confidence is not a general protein stability predictor
- prediction/confidence
- prediction/stability-expression
Jul 28, 2026
Antibody LMs are worse for expression prediction than generic PLMs
Jul 28, 2026
Random splits overestimate protein language model generalization on antibody expression prediction
- evidence/generalization
- prediction/stability-expression
Jul 28, 2026
Thermostability prediction from protein language model representations peaks in the last few layers
- prediction/stability-expression
- inference/feature-extraction
Jul 28, 2026
Training antibody language models on normalized mutation frequencies improves zero-shot expression prediction
Jul 20, 2026
Experimentally successful miniprotein binders have higher predicted stability
Jul 20, 2026
Most computational protein-stability metrics correlate poorly with experimental dG
- prediction/stability-expression
- evidence/design-validation
Jul 20, 2026
PLM pseudoperplexity indicates stability-prediction accuracy
- prediction/confidence
- prediction/stability-expression
May 06, 2026
Inverse folding model logits can zero-shot predict expression changes arising from in antibody CDRs in cases where ground truth structure is known
- prediction/stability-expression
- design/inverse-folding
Apr 21, 2026
A subset of residues is sufficient to predict protein dG
- prediction/stability-expression
Apr 21, 2026
Abs modeled using MD are better for featurization than those modeled using homology modeling
- prediction/stability-expression
- biophysics/molecular-simulation
Apr 21, 2026
Adding structural adaptors to language models leads to improvements in thermostability prediction compared to structure-based NNs alone
Apr 21, 2026
All-atom scoring functions, but not backbone-only scoring functions, correlate with protein stability
- prediction/stability-expression
Apr 21, 2026
Antibody LMs outperform generic PLMs on intrafamily thermostability prediction
- prediction/stability-expression
- inference/feature-extraction
Apr 21, 2026
Antibody developability parameters predicted from sequence are more correlated with each other than those predicted from structure
- prediction/stability-expression
- design/developability
Apr 21, 2026
Antibody developability predictions are relatively stable to single point mutations
- prediction/stability-expression
- design/developability
Apr 21, 2026
Antibody developability predictions from computational models are sensitive to the structure prediction method
Apr 21, 2026
Averaging logits from multiple sources can improve fitness prediction
Apr 21, 2026
Biophysical models trained on single and double point mutations can predict effects of three or more mutations on stability
Apr 21, 2026
Features for antibody property prediction derived from MD simulations outperform those from language models and static structures
Apr 21, 2026
Free energy perturbation
Apr 21, 2026
Larger PLMs are better at thermostability prediction
- prediction/stability-expression
- training/pretraining-and-scaling
Apr 21, 2026
MD trajectories reproduce experimental dG values to within 1 kcal per mol
- biophysics/molecular-simulation
- prediction/stability-expression
Apr 21, 2026
MSA-based PLMs outperform generic PLMs on predicting structure and stability
Apr 21, 2026
PLMs are better at reproducing sequence-based developability predictions than structure-based predictions
- prediction/stability-expression
- inference/feature-extraction
Apr 21, 2026
Protein structure prediction and design metrics don't correlate with expression probability
Apr 21, 2026
Randomly masking residues prior to running ESMFold allows false positives to be identified more effectively
Apr 21, 2026
Residue conservation and solvent exposure data perform comparably to PLMs at some property prediction tasks
Apr 21, 2026
Structural modeling introduces bias toward larger hydrophobic patches in antibodies
Apr 21, 2026
Structure-based methods outperform sequence-based methods on protein stability prediction of point mutants, but not full sequences
- prediction/stability-expression
- inference/feature-extraction
Apr 21, 2026
Unfolding cooperativity is more difficult to predict than protein stability
- prediction/stability-expression
- biophysics/folding
Apr 21, 2026
ddG predictions calculated from AlphaFold structures are equally accurate as those derived from experimental structures
- prediction/stability-expression
- evidence/generalization
Apr 21, 2026
About 100k datapoints required to train accurate ddG predictor
- prediction/stability-expression
- evidence/datasets
Apr 21, 2026
Antibody sequence similarity is not correlated with developability similarity
- design/developability
- prediction/stability-expression
Apr 21, 2026
Biophysical models outperform linear models for stability prediction
- prediction/stability-expression
- prediction/variant-effects
Apr 21, 2026
DNA sequence entropy is strongly predictive of protein expression
- prediction/stability-expression
- design/developability
Apr 21, 2026
Including optimal growth temperature during pre-training of PLMs improves prediction and design of thermostability
Apr 20, 2026
Stability and thermostability

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