Quartz 4

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Measurements

Created Sep 26, 2026Modified Sep 07, 2026

Assay definitions, reproducibility, experimental artifacts, structural evidence, and interpretation of evaluation statistics.

39 items with this tag.

Aug 25, 2026
NGS sequence abundance does not correlate with binding affinity
- evidence/measurements
- design/directed-evolution
Aug 19, 2026
Clonal expansion correlates with antigen binding
Aug 19, 2026
Conventional NMR structure bundles are not thermodynamic ensembles
- evidence/measurements
- biophysics/ensemble-analysis
Aug 19, 2026
ROC-AUC is prevalence-invariant but does not measure deployment precision
- evidence/measurements
Jul 28, 2026
Large-scale measurements, such as Kd and IC50, from different assays correlate weakly in different studies
- evidence/measurements
- prediction/binding
Jul 28, 2026
Protein backbone design diffusion models can be repurposed for fitting structures into electron density
Jul 17, 2026
Aggregate benchmark correlations can mask weak within-category performance
- evidence/measurements
- prediction/variant-effects
Jul 17, 2026
Cell-free systems have higher expression rates for minibinders than cell-based systems
Jul 17, 2026
Distinct fitness measurements of the same variants of the same protein vary wildly in Spearman
- evidence/measurements
- prediction/variant-effects
Jun 23, 2026
TM-score
- evidence/measurements
- prediction/confidence
Apr 21, 2026
Diffusion-based structure prediction can be steered by modifying the conditioning embeddings rather than the latent space, and such embeddings can be used for subsequent iterations
Apr 21, 2026
Computational models of proteins fit NMR data better than models designed using classical approaches
- prediction/structure
- evidence/measurements
Apr 21, 2026
Display methods
- design/directed-evolution
- evidence/measurements
Apr 21, 2026
DockQ
- evidence/measurements
- prediction/complexes
Apr 21, 2026
Ensembles can be modeled by structure prediction NNs using experimental data via guidance sampling
Apr 21, 2026
Most commercially available tool antibodies are nonspecific
- antibodies/recognition
- evidence/measurements
Apr 21, 2026
Next-generation sequencing
- evidence/measurements
- antibodies/repertoires
Apr 21, 2026
Precision decreases and recall increases as variant effect prediction focuses on top-performing point mutations
- prediction/variant-effects
- evidence/measurements
Apr 21, 2026
Sequence recovery using inverse folding is lower on NMR structures than crystal structures
- design/inverse-folding
- evidence/measurements
Apr 21, 2026
Structural modeling introduces bias toward larger hydrophobic patches in antibodies
Apr 21, 2026
Structure ensemble prediction methods are unable to accurately model subtle conformational differences captured by X-ray crystallography
- prediction/ensembles
- evidence/measurements
Apr 21, 2026
The PDB already contains implicit information about conformational dynamics based on subtle differences in closely related structures
- evidence/measurements
- biophysics/ensemble-analysis
Apr 21, 2026
Variant effect prediction quality correlates with DMS prediction quality
- prediction/variant-effects
- evidence/measurements
Apr 21, 2026
Cooling samples for cryogenic crystallography or cryo-EM narrows the conformational ensemble
- evidence/measurements
- biophysics/ensemble-analysis
Apr 21, 2026
Cryo-EM particle counting does not reliably provide true Boltzmann distributions of molecules
- evidence/measurements
- biophysics/ensemble-analysis
Apr 21, 2026
Crystal structures can have nonphysiological salt bridges
- evidence/measurements
- biophysics/interactions
Apr 21, 2026
D2O has a stabilizing effect on protein structure
- evidence/measurements
- biophysics/stability
Apr 21, 2026
Gaussian processes can identify false positives
- evidence/measurements
Apr 21, 2026
High predicted aligned error correlates with violation of experimental distance measurements
- prediction/confidence
- evidence/measurements
Apr 21, 2026
Ligand-binding sites fit experimental electron density better than other parts of protein structures
- evidence/measurements
- prediction/ligand-docking
Apr 21, 2026
Lipid and detergent composition affects the conformational landscape of membrane proteins
- biophysics/dynamics
- evidence/measurements
Apr 21, 2026
MD force fields can be screened for agreement with experimental data
- biophysics/molecular-simulation
- evidence/measurements
Apr 21, 2026
Mega-scale dataset is inaccurate for DNA-binding domains
- evidence/measurements
- evidence/datasets
Apr 21, 2026
Protein denaturation cooperativity varies depending on whether it is thermally, chemically, or pressure induced
- biophysics/folding
- evidence/measurements
Apr 21, 2026
Spearman correlations of protein property prediction methods do not correlate perfectly with absolute error
- evidence/measurements
Apr 21, 2026
X-ray density can capture alternate conformations of proteins and their ligands
- evidence/measurements
- biophysics/ensemble-analysis
Apr 20, 2026
Binary classifiers
- evidence/measurements
Apr 20, 2026
Kd differs from IC50, LD50, and GI50
- evidence/measurements
- prediction/binding
Nov 04, 2024
Fréchet distance
- evidence/measurements
- evidence/design-validation

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