Quartz 4

Tag: antibody-antigen-interactions

Binding affinity

15 items with this tag.

Jul 28, 2026
AF3 binding affinity predictions are orthogonal to those made by force fields and other neural networks
- alphafold3
- antibody-antigen-interactions/binding-affinity
Jul 20, 2026
Explicit germline encoding improves zero-shot antibody-affinity prediction
- protein-language-models/antibodies
- antibody-antigen-interactions/binding-affinity
Apr 28, 2026
Subset of mutations obtained during affinity maturation contribute disproportionately to affinity
- affinity-maturation
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Affinity-specificity tradeoff in antibodies is partially mediated by varying the magnitude of rigidification
Apr 21, 2026
Agonist antibodies benefit from low affinity due to antigen clustering
Apr 21, 2026
Antibodies and BCRs have different binding kinetics
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Antibody affinity can be improved by stabilization
- affinity-maturation
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Antibody on and off rates are capped by the affinity maturation process
- affinity-maturation
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Binding affinity of protein-protein interactions correlates with buried surface area
- protein-protein-interactions
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Conformational entropy in antibodies is inversely proportional to antigen affinity
Apr 21, 2026
Generic PLMs outperform antibody-specific PLMs on zero-shot predictions of affinity changes
Apr 21, 2026
Germline precursors bind to their antigens with nanomolar affinity
- affinity-maturation
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Inverse folding models can predict antibody-antigen binding affinities with higher accuracy by correcting with predictions from unbound state
- antibody-structure-prediction/complex-prediction
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Lower antibody affinity is desirable for minimizing on-target off-tumor binding
- affinity-maturation
- antibody-antigen-interactions/binding-affinity
Apr 21, 2026
Mutations obtained by antibodies during affinity maturation show epistasis in biophysical properties but not binding

Complex prediction

18 items with this tag.

Jul 17, 2026
Antibody-antigen complex prediction scales with training data and compute
- antibody-antigen-interactions/complex-prediction
Jul 17, 2026
Different AlphaFold3 clones have differently calibrated confidence heads
Jul 17, 2026
Interface contact score
Jul 17, 2026
Antibody structure prediction improved with AlphaFold2 features
Apr 28, 2026
AlphaFold3 ipTM can distinguish between antibody binders and nonbinders
Apr 21, 2026
Ab-Ag inverse folding methods benefit from pretraining
- inverse-folding/training
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
AlphaFold2 recapitulates interaction biases from PDB when modeling antibodies
- alphafold2
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
Antigen context improves CDRH3 structure prediction
- structure-prediction/complex-prediction
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
Correct CDRH3 prediction is necessary but insufficient for correct Ab-Ag docking
- structure-prediction/complex-prediction
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
Correct antibody-antigen prediction in AF3 and related models is partially determined by training set similarity
Apr 21, 2026
Dropout improves AF2 multimer prediction, including for antibody-antigen complexes
- alphafold2
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
Increasing diffusion samples is sufficient to yield correctly predicted antibody-antigen complexes
Apr 21, 2026
LM-based antibody structure prediction methods work equally well with generic and Ab PLMs
Apr 21, 2026
No one-size-fits-all approach to scoring antibody structures
Apr 21, 2026
PAE weakly correlates with Ab-Ag binding
Apr 21, 2026
Structure-based methods outperform sequence-based methods on antigen-dependent antibody design
Apr 21, 2026
The structures of nanobodies with kinked CDR3 loops are more difficult to predict in complex with their antigen
- antibody-structure-prediction/complex-prediction
- antibody-antigen-interactions/complex-prediction
Apr 21, 2026
Variable regions can adopt multiple interchain orientations, and these are difficult to predict
- structure-prediction/limitations
- antibody-antigen-interactions/complex-prediction

Misc

15 items with this tag.

Jul 17, 2026
Conformational entropy in antibodies decreases during affinity maturation
Apr 21, 2026
Affinity maturation causes antibody-antigen interfaces to be more similar to generic PPI interfaces
Apr 21, 2026
Affinity matured antibodies can adopt distinct binding poses from germline precursors
- affinity-maturation
- antibody-antigen-interactions/misc
Apr 21, 2026
Antibodies from different repertoires within a given species targeting the same epitope often have the same light chain isotype and share critical residues
- affinity-maturation/somatic-hypermutation
- antibody-antigen-interactions/misc
Apr 21, 2026
Antibody-antigen binding modes are not necessarily defined by induced fit
- protein-protein-interactions
- antibody-antigen-interactions/misc
Apr 21, 2026
CDR3 far more likely to be part of paratope of nanobodies compared to antibodies
- cdrh3
- antibody-antigen-interactions/misc
Apr 21, 2026
CDR3 loops encode specificity while CDR1 and CDR2 encode cross-reactivity
Apr 21, 2026
CDRH3 conformational rigidity reduces cross reactivity
Apr 21, 2026
CDRH3 has most contacts with antigen
Apr 21, 2026
CDRH3 is necessary but insufficient to guarantee binding to a particular epitope
- cdrh3
- antibody-antigen-interactions/misc
Apr 21, 2026
Changes to hydrophobicity and charge correlate with antibody escape
- antibody-developability/hydrophobicity
- antibody-antigen-interactions/misc
Apr 21, 2026
Most nanobodies do not bind using all three CDRs
- antibodies/nanobodies
- antibody-antigen-interactions/misc
Apr 21, 2026
Nanobodies and Abs target different epitopes but with similar accessibility and number of contacts
- antibodies/nanobodies
- antibody-antigen-interactions/misc
Apr 21, 2026
Nanobody framework residues more likely to be part of paratope than those of antibodies
- antibodies/nanobodies
- antibody-antigen-interactions/misc
Apr 21, 2026
Up to 22 percent of antigen binding residues are outside CDRs
- antibody-antigen-interactions/misc

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