Quartz 4

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Structure

Created Sep 26, 2026Modified Sep 07, 2026

Predicting protein structures, contacts, sidechains, and structural refinement; includes relevant tool/reference notes.

60 items with this tag.

Sep 07, 2026
ESMFold has massive activations that disproportionately contribute to output quality
- model-analysis/interpretability
- prediction/structure
Jul 28, 2026
MSA protein language models can identify intermolecular contacts
- prediction/structure
- prediction/complexes
Jul 28, 2026
Query-conditioned outer product
- model-design/architectures
- prediction/structure
Jul 20, 2026
AF3-generation methods incorporate MSA information exclusively into the pair representation
- model-analysis/interpretability
- prediction/structure
Jul 20, 2026
AlphaFold3 inference benefits more from phylogenetically diverse MSAs than deep redundant MSAs
Jul 20, 2026
MSA-conditioned AlphaFold3 representations compress as the Pairformer proceeds
- model-analysis/representation-geometry
- prediction/structure
Jul 20, 2026
MSAs make AlphaFold3 predictions robust to extensive mutation and deletion
Jul 20, 2026
Removing MSAs collapses AlphaFold3's latent space
- model-analysis/representation-geometry
- prediction/structure
Apr 21, 2026
AlphaFold2 generalizes to unseen secondary structures and topologies
- evidence/generalization
- prediction/structure
Apr 21, 2026
AlphaFold3 uses cross-distillation from AlphaFold2 to avoid hallucinating secondary structure in low-pLDDT regions
- evidence/datasets
- prediction/structure
Apr 21, 2026
Categorical Jacobian method
- prediction/structure
- model-analysis/interpretability
Apr 21, 2026
Computational models of proteins fit NMR data better than models designed using classical approaches
- prediction/structure
- evidence/measurements
Apr 21, 2026
DL structure tools introduce chiral errors such as swapped chiral centers, D-amino acids, and cis-amide bonds
- prediction/structure
- prediction/antibody-structure
Apr 21, 2026
De novo designed proteins with alpha helices are easier to predict than those with other secondary structures
Apr 21, 2026
Deep learning methods outperform classical methods on sidechain prediction
- prediction/structure
Apr 21, 2026
Distance between averaged PLM embeddings does not correlate with structural difference
- model-analysis/representation-geometry
- prediction/structure
Apr 21, 2026
Diverse MSAs are better for training structure prediction neural networks than random MSAs
- evidence/datasets
- prediction/structure
Apr 21, 2026
ESMFold
- prediction/structure
Apr 21, 2026
Evoformer
- model-design/architectures
- prediction/structure
Apr 21, 2026
Fine-tuning AlphaFold for MHC prediction by adding Evoformer layers improves RMSD and pLDDT
- training/fine-tuning
- prediction/structure
Apr 21, 2026
Fine-tuning base models on test cases can improve the performance of variant effect and structure prediction
Apr 21, 2026
Frame aligned point error
- training/objectives-and-optimization
- prediction/structure
Apr 21, 2026
IPA-based structure prediction neural networks train sequentially along three spatial axes
- training/pretraining-and-scaling
- prediction/structure
Apr 21, 2026
Increasing RosettaFold embedding dimension improves structure prediction
- model-design/architectures
- prediction/structure
Apr 21, 2026
Iterative structure prediction outperforms all-at-once structure prediction
- prediction/structure
- inference/sampling-and-search
Apr 21, 2026
Language-based protein folding NNs predict novelty with far lower confidence than MSA-based protein folding NNs
- evidence/generalization
- prediction/structure
Apr 21, 2026
MSA-based PLMs outperform generic PLMs on predicting structure and stability
Apr 21, 2026
MSA-based structure predictions outperform PLM-based methods
- prediction/structure
Apr 21, 2026
Membrane proteins are predicted by PLMs via solvent-exposed hydrophobic residues
- model-analysis/interpretability
- prediction/structure
Apr 21, 2026
OmegaFold
- prediction/structure
- prediction/antibody-structure
Apr 21, 2026
PLM attention matrices correspond to 3D contacts
- model-analysis/interpretability
- prediction/structure
Apr 21, 2026
Protein folding neural networks can be subject to adversarial attacks
- evidence/generalization
- prediction/structure
Apr 21, 2026
Protein folding neural networks do not extrapolate to new ligand binding sites
- evidence/generalization
- prediction/structure
Apr 21, 2026
Protein folding neural networks do not learn the physics of protein folding for most proteins
Apr 21, 2026
Protein folding neural networks make local optimizations in the absence of coevolutionary information
- model-analysis/interpretability
- prediction/structure
Apr 21, 2026
Protein language models and PLM-based structure prediction generalize to de novo designed proteins
Apr 21, 2026
Protein structure prediction methods predict idealized secondary structures in de novo proteins
- prediction/structure
- evidence/design-validation
Apr 21, 2026
PyMOL
- prediction/structure
Apr 21, 2026
RMSD is a poor training objective for structure prediction
- training/objectives-and-optimization
- prediction/structure
Apr 21, 2026
Scrambled MSAs outperform single-sequence-prediction with AlphaFold
- prediction/structure
- inference/conditioning
Apr 21, 2026
Self-distillation exposes more data to Evoformer
- evidence/datasets
- prediction/structure
Apr 21, 2026
Sequence perplexity and TM-score are negatively correlated when predicting structure using protein language models
- prediction/confidence
- prediction/structure
Apr 21, 2026
SimpleFold
Apr 21, 2026
Structure prediction with AlphaFold improved when starting from an initial guess, rather than default initialization
Apr 21, 2026
The structures of shorter de novo designed sequences are easier to predict than those of longer proteins
- prediction/structure
- evidence/design-validation
Apr 21, 2026
Triangular updates are dispensable for structure prediction
- model-design/architectures
- prediction/structure
Apr 21, 2026
Unfolded and nonfunctional isoforms of folded proteins are incorrectly predicted as folded by protein folding neural networks
- evidence/generalization
- prediction/structure
Apr 21, 2026
Unfreezing PLM during structure training improves prediction quality
- training/fine-tuning
- prediction/structure
Apr 21, 2026
Flow matching and diffusion perform comparably for biomolecular structure prediction
- prediction/structure
- model-design/generative-models
Apr 21, 2026
Invariant point attention is dispensable to structure prediction
- model-design/architectures
- prediction/structure
Apr 21, 2026
De novo structure prediction with ligands outperforms apo de novo structure prediction alone
Apr 21, 2026
Including crystal contacts in training data improves sidechain prediction
- prediction/structure
- evidence/datasets
Apr 21, 2026
Information about backbone atoms is lost when rebuilding full-atom protein models from alpha carbon trace alone
- prediction/structure
- design/inverse-folding
Apr 21, 2026
Memorization in protein structure prediction
- evidence/generalization
- prediction/structure
Apr 20, 2026
AlphaFold2
- prediction/structure
- model-design/architectures
Apr 20, 2026
AlphaFold3
Apr 20, 2026
RoseTTAFold
- prediction/structure
- model-design/architectures
Apr 20, 2026
Structure prediction
- prediction/structure
Apr 20, 2026
Top2018
- evidence/datasets
- prediction/structure
Apr 10, 2026
Rosetta
- design/sequence-generation
- prediction/structure

Created with Quartz v4.5.2 © 2026

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