Found 66 total tags.
Antibodies are proteins with two heavy chains and two light chains produced by B cells, central to the adaptive immune system. Their structure consists of a variable region (containing CDRs and a framework region) and three constant regions (CH1, CH2, CH3). The variable region and CH1 form the Fab, while the remainder forms the Fc region. B cell receptors are antibodies with an additional CH4 domain.
IgA is found in mucous membranes, cannot activate the complement system, and makes up roughly two-thirds of antibodies in healthy adults. It is notable for being double-sided.
IgE has only one binding site, mainly protects against large organisms like parasites, and is responsible for allergic reactions.
IgG is the standard antibody class used in therapeutic design. Cannot activate the complement system and can pass through the placenta.
IgM is far less subject to affinity maturation than IgG, responds to lipids and polysaccharides, and activates the complement system.
SAbDab is a database of all antibody and nanobody structures in the PDB. The full list can be downloaded with:
curl -s https://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/sabdab/summary/all/130 items with this tag. Showing first 10 tags.
CDR and framework organization, heavy/light-chain pairing, loop geometry, numbering, and antibody formats as structures.
51 items with this tag. Showing first 10 tags.
Somatic mutation and selection during in-vivo affinity maturation, including effects on stability, specificity, and expression. Laboratory optimization goes under design.
30 items with this tag. Showing first 10 tags.
Findings specific to single-domain antibodies, especially their differences from conventional antibodies; do not add merely because a generic method was tested on one VHH.
25 items with this tag. Showing first 10 tags.
Paratopes, epitopes, binding modes, cross-reactivity, and the molecular basis of antibody recognition.
39 items with this tag. Showing first 10 tags.
Repertoire diversity, germline usage, V(D)J recombination, chain pairing across populations, and sequencing-derived repertoire patterns.
26 items with this tag. Showing first 10 tags.
Physical properties and mechanisms connecting protein sequence, structure, dynamics, binding, and catalysis.
172 items with this tag. Showing first 10 tags.
Catalytic mechanisms, active-site organization, substrate turnover, and enzyme function.
12 items with this tag. Showing first 10 tags.
Conformational equilibria, flexibility, allostery, and their functional consequences.
39 items with this tag. Showing first 10 tags.
Inferring populations, kinetics, collective variables, and reduced descriptions from ensembles or trajectories.
16 items with this tag. Showing first 10 tags.
Physical folding and unfolding pathways, rates, cooperativity, and intermediates; not the computational task of predicting a structure.
19 items with this tag. Showing first 10 tags.
Physical determinants of binding, specificity, interfaces, oligomerization, and assembly.
31 items with this tag. Showing first 10 tags.
Molecular dynamics, force fields, simulation setup, and enhanced sampling of physical trajectories.
25 items with this tag. Showing first 10 tags.
What determines thermodynamic or thermal stability, and how stability couples to other properties. Keep melting temperature, folding free energy, and kinetic stability distinct in the notes.
44 items with this tag. Showing first 10 tags.
Free energies, statistical ensembles, partition functions, and the mathematical foundations of equilibrium sampling.
11 items with this tag. Showing first 10 tags.
Immune signaling and cellular mechanisms relevant to protein therapeutics.
31 items with this tag. Showing first 10 tags.
Immune cells, antigen presentation, cytokines, receptors, and signaling biology.
22 items with this tag. Showing first 10 tags.
How therapeutics act: receptor modulation, multivalency, payload delivery, targeted degradation, and circulation or clearance mechanisms.
15 items with this tag. Showing first 10 tags.
Engineering sequences, folds, binding, catalytic function, and properties that make proteins useful.
224 items with this tag. Showing first 10 tags.
Computational antibody discovery, CDR design, and in-vitro or in-silico affinity optimization.
33 items with this tag. Showing first 10 tags.
Generating backbones, folds, and motif scaffolds; includes designability and structural-diversity limitations.
33 items with this tag. Showing first 10 tags.
Designing non-antibody protein binders and cross-format binder workflows; antibody-only work goes under design/antibodies.
10 items with this tag.
Expression, solubility, nonspecific binding, self-association, immunogenicity, humanization, and other constraints on making usable protein products.
49 items with this tag. Showing first 10 tags.
Iterative experimental optimization, library design, mutagenesis, selection, and model-guided experimental search.
25 items with this tag. Showing first 10 tags.
Engineering catalytic activity, enzyme specificity, active sites, and functional enzyme designs.
16 items with this tag. Showing first 10 tags.
Designing or scoring amino-acid sequences conditioned on a structure or structural ensemble; includes inverse-folding training and applications to property prediction.
55 items with this tag. Showing first 10 tags.
Domain insertion, fusion, oligomerization modules, and engineering proteins as structural or functional tools.
13 items with this tag. Showing first 10 tags.
Generating and optimizing sequences with sequence models, evolutionary profiles, or hallucination, including general sequence-search strategies. Fixed-structure sequence design goes under design/inverse-folding.
25 items with this tag. Showing first 10 tags.
Dataset composition, generalization, experimental validation, and the interpretation of measurements.
181 items with this tag. Showing first 10 tags.
Dataset resources, composition, clustering, taxonomic bias, negative examples, synthetic data, and coverage.
52 items with this tag. Showing first 10 tags.
Whether computational design scores, refolding tests, or rankings predict useful experimental outcomes; includes appropriate prospective and baseline comparisons.
48 items with this tag. Showing first 10 tags.
Memorization, leakage, out-of-distribution performance, shortcuts, robustness, and when apparent progress does not transfer.
49 items with this tag. Showing first 10 tags.
Assay definitions, reproducibility, experimental artifacts, structural evidence, and interpretation of evaluation statistics.
39 items with this tag. Showing first 10 tags.
Selection, mutation effects, ancestry, and homology across natural and engineered proteins.
115 items with this tag. Showing first 10 tags.
Ancestral reconstruction, consensus sequences, historical inference, and their uses in engineering.
14 items with this tag. Showing first 10 tags.
Homology detection, sequence and structural alignment, remote similarity, and conservation across related proteins.
21 items with this tag. Showing first 10 tags.
Biological effects of substitutions and indels, fitness landscapes, epistasis, and accessible evolutionary paths. Prediction algorithms go under prediction/variant-effects.
47 items with this tag. Showing first 10 tags.
Natural selection, evolutionary constraints, adaptation, evolvability, and the natural distribution of sequence and fold space.
44 items with this tag. Showing first 10 tags.
How to obtain useful outputs from existing models through conditioning, feature extraction, sampling, guidance, and ensembling.
88 items with this tag. Showing first 10 tags.
How runtime inputs such as MSAs, homolog prompts, templates, ligands, and initial structures affect predictions. Active reward-driven changes to conditioning also belong under inference/guidance.
15 items with this tag. Showing first 10 tags.
Combining predictions, scores, prompts, or samples from multiple model runs. Weight merging is documented separately under training/fine-tuning.
6 items with this tag.
Using learned embeddings, attention-derived features, pooling, or probes for downstream prediction and retrieval. A frozen base model may supply features to a separately trained head.
29 items with this tag. Showing first 10 tags.
Steering a fixed model with rewards, constraints, gradients, activation edits, or importance reweighting. Backpropagation to an input is not model fine-tuning.
26 items with this tag. Showing first 10 tags.
Exploring candidate sequences, structures, or designs through sampling, recycles, decoding order, search algorithms, and increased inference compute. Physical MD sampling stays under biophysics/molecular-simulation.
14 items with this tag. Showing first 10 tags.
What models represent internally, how that information is organized, and how it affects their behavior.
42 items with this tag. Showing first 10 tags.
What models internally encode and how they use it: attention analysis, layer-wise probing, sparse autoencoders, and mechanistic explanations. Generalization tests remain under evidence/generalization.
29 items with this tag. Showing first 10 tags.
How similarities, clusters, distances, and manifolds in model representations relate to sequence, structure, or function. Practical feature extraction is a separate inference topic.
14 items with this tag. Showing first 10 tags.
How models are constructed: network architectures, multimodal representations, and generative formulations.
75 items with this tag. Showing first 10 tags.
Network components and architecture choices, including attention, equivariance, graph networks, and computational efficiency.
36 items with this tag. Showing first 10 tags.
Diffusion, flow matching, VAEs, and energy-based generative formulations. Pair with the substantive design or prediction task when relevant.
21 items with this tag. Showing first 10 tags.
Combining sequence, structure, or other modalities; structural tokenization, feature fusion, and hybrid models.
24 items with this tag. Showing first 10 tags.
What can be predicted about proteins, and how confidence relates to the quantity being predicted.
287 items with this tag. Showing first 10 tags.
Predicting isolated antibody and nanobody structures, CDR conformations, and interdomain orientations.
22 items with this tag. Showing first 10 tags.
Predicting affinity, binding versus nonbinding, specificity, and ligand-binding residues; does not imply a predicted complex geometry.
26 items with this tag. Showing first 10 tags.
Predicting macromolecular complex geometry, including antibody-antigen complexes and oligomer stoichiometry; distinct from predicting affinity.
29 items with this tag. Showing first 10 tags.
What model confidence scores and uncertainty estimates mean, how they are calibrated, and what they fail to predict.
47 items with this tag. Showing first 10 tags.
Predicting multiple conformations, populations, or conformational landscapes with learned models.
33 items with this tag. Showing first 10 tags.
Predicting functional annotations, catalytic activity, and enzyme specificity.
10 items with this tag.
Predicting small-molecule binding pockets and poses, including co-folding; distinct from affinity prediction.
13 items with this tag. Showing first 10 tags.
Predicting stability, folding cooperativity, expression, solubility, and related physical developability properties.
40 items with this tag. Showing first 10 tags.
Predicting protein structures, contacts, sidechains, and structural refinement; includes relevant tool/reference notes.
60 items with this tag. Showing first 10 tags.
Predicting mutation-induced effects on fitness or pathogenicity. Add a property-specific tag only when that property is a substantive focus.
53 items with this tag. Showing first 10 tags.
How models are trained and adapted: pretraining, fine-tuning, objectives, optimization, and scaling.
88 items with this tag. Showing first 10 tags.
Updating or adapting pretrained parameters: fine-tuning, adapters, forgetting, transfer, and combining task-specific weights. Test-time parameter updates still belong here.
35 items with this tag. Showing first 10 tags.
Training losses, auxiliary objectives, regularization, optimization schedules, and gradient estimators. Optimizing inputs through frozen models belongs under inference/guidance.
21 items with this tag. Showing first 10 tags.
Pretraining objectives, masking, model/data/compute scaling, and foundation-model learning dynamics. Dataset composition is covered by evidence/datasets when central.
39 items with this tag. Showing first 10 tags.