| { |
| "schema": "frontierlab.method-evaluation.v1", |
| "context_id": "ee7f790ba48474bb63a935f6108f1e698121a404d93a5bf0389946ba2932dcf8", |
| "status": "READY_FOR_DRAFT_PLANNING", |
| "origin": "RESEARCHER_ASSESSED", |
| "candidates": [ |
| { |
| "candidate_id": "M1", |
| "name": "Directed evolution with yeast surface display and alternating-pH selection", |
| "evidence_ids": [ |
| "PMC4314675" |
| ], |
| "scope": "Use a displayed Fcab library with positive selection for Her2 binding at pH 7.4 and negative selection/non-binding at pH 6.0, followed by clone-level pH-dependent binding characterization.", |
| "checks": { |
| "data": { |
| "status": "unknown", |
| "detail": "Underlying clone-level screening and selection datasets have not been independently retrieved for FrontierLab.", |
| "reference": "" |
| }, |
| "code": { |
| "status": "not_applicable", |
| "detail": "The evaluated route is primarily an experimental directed-evolution workflow; no required computational code artifact has been established from the current source review.", |
| "reference": "" |
| }, |
| "environment": { |
| "status": "unknown", |
| "detail": "Laboratory platform details and instrument settings have not been independently normalized into a reproducible FrontierLab environment record.", |
| "reference": "" |
| }, |
| "parameters": { |
| "status": "documented", |
| "detail": "The source-derived comparison identifies alternating selection at pH 7.4 for binding and pH 6.0 for non-binding as central design parameters.", |
| "reference": "PMC4314675 / doi:10.1002/biot.201300483" |
| }, |
| "protocol": { |
| "status": "documented", |
| "detail": "The published study reports directed evolution using yeast surface display followed by characterization of isolated pH-sensitive Fcab variants.", |
| "reference": "PMC4314675 / doi:10.1002/biot.201300483" |
| }, |
| "metrics": { |
| "status": "documented", |
| "detail": "The source reports pH-dependent binding characterization and downstream assessment of isolated variants; FrontierLab has not reproduced these measurements.", |
| "reference": "PMC4314675 / doi:10.1002/biot.201300483" |
| } |
| }, |
| "comparison": { |
| "expected_value": "Explores sequence space without requiring a predefined histidine-centered mechanism and can reveal non-obvious pH-switching variants.", |
| "resources": "Requires a physical display library, sorting workflow, recombinant target and downstream clone expression and characterization.", |
| "validation": "Compare binding across acidic and physiological pH, then verify isolated variants with independent soluble-protein or cell-based assays.", |
| "limitations": "Experimentally intensive and sensitive to library composition, target format, selection pressure and sorting thresholds; AI is supportive rather than central to the core search loop.", |
| "novelty": "Strong comparator for mechanism diversity because the reported Fcab examples include pH-sensitive variants without histidine mutations." |
| }, |
| "reproducibility_status": "INCOMPLETE_DOCUMENTATION", |
| "open_checks": [ |
| { |
| "item": "data", |
| "status": "unknown", |
| "reason": "Underlying clone-level screening and selection datasets have not been independently retrieved for FrontierLab." |
| }, |
| { |
| "item": "environment", |
| "status": "unknown", |
| "reason": "Laboratory platform details and instrument settings have not been independently normalized into a reproducible FrontierLab environment record." |
| } |
| ] |
| }, |
| { |
| "candidate_id": "M2", |
| "name": "Structure-based dual-pH histidine-scanning computational design", |
| "evidence_ids": [ |
| "PMC6927761" |
| ], |
| "scope": "Use an antibody-antigen structural model to perform dual-pH histidine-scanning design, prioritize variants in silico, and then validate Fab, cell-surface and full-antibody behavior across acidic and physiological pH.", |
| "checks": { |
| "data": { |
| "status": "unknown", |
| "detail": "The complete design inputs, intermediate candidate-ranking outputs and raw validation datasets have not yet been independently packaged for FrontierLab.", |
| "reference": "" |
| }, |
| "code": { |
| "status": "unknown", |
| "detail": "Availability and reproducibility of the original ADAPT implementation or an equivalent executable design stack have not yet been independently verified.", |
| "reference": "" |
| }, |
| "environment": { |
| "status": "unknown", |
| "detail": "The exact computational environment, protonation/modeling settings and dependency versions have not yet been reconstructed.", |
| "reference": "" |
| }, |
| "parameters": { |
| "status": "documented", |
| "detail": "The source-derived method centers on structure-based dual-pH histidine scanning and comparison of acidic versus physiological pH binding behavior.", |
| "reference": "PMC6927761 / doi:10.1080/19420862.2019.1682866" |
| }, |
| "protocol": { |
| "status": "documented", |
| "detail": "The published workflow links computational design to Fab and full-antibody validation, including cell-based and functional assays.", |
| "reference": "PMC6927761 / doi:10.1080/19420862.2019.1682866" |
| }, |
| "metrics": { |
| "status": "documented", |
| "detail": "Reported validation includes pH-dependent binding/selectivity readouts; FrontierLab has not reproduced these measurements and must treat apparent cell-binding affinity cautiously where avidity or stoichiometry can confound interpretation.", |
| "reference": "PMC6927761 / doi:10.1080/19420862.2019.1682866" |
| } |
| }, |
| "comparison": { |
| "expected_value": "Provides a targeted in-silico-to-in-vitro design path in which AI can assist structure interpretation, candidate prioritization and explicit reasoning over pH-dependent design constraints before laboratory validation.", |
| "resources": "Requires a structural model, a reproducible design implementation or equivalent computational stack, recombinant expression and orthogonal binding and functional validation.", |
| "validation": "Validate prioritized variants across pH using Fab-level measurements, cell-based assays and full-antibody tests; add an orthogonal biophysical assay such as SPR on monomeric Fab where feasible to separate intrinsic affinity from avidity effects.", |
| "limitations": "Depends on structural-model quality and a histidine-centered search assumption; apparent cell-binding affinity can be influenced by avidity/stoichiometry, so orthogonal validation is required before mechanistic interpretation.", |
| "novelty": "Best fit for the FrontierLab demo because it exposes a complete AI-assisted design-to-validation chain while making uncertainty, experimental handoff and falsification visible." |
| }, |
| "reproducibility_status": "INCOMPLETE_DOCUMENTATION", |
| "open_checks": [ |
| { |
| "item": "data", |
| "status": "unknown", |
| "reason": "The complete design inputs, intermediate candidate-ranking outputs and raw validation datasets have not yet been independently packaged for FrontierLab." |
| }, |
| { |
| "item": "code", |
| "status": "unknown", |
| "reason": "Availability and reproducibility of the original ADAPT implementation or an equivalent executable design stack have not yet been independently verified." |
| }, |
| { |
| "item": "environment", |
| "status": "unknown", |
| "reason": "The exact computational environment, protonation/modeling settings and dependency versions have not yet been reconstructed." |
| } |
| ] |
| } |
| ], |
| "selected_candidate_id": "M2", |
| "rationale": "Researcher selected M2 because its structure-based computational design creates the clearest in-silico-to-in-vitro AI-for-Science demonstration: an AI agent can reason over a structural model, prioritize dual-pH histidine-scanning variants, and hand candidates to experimental Fab, cell, full-antibody and functional validation. This produces a stronger end-to-end FrontierLab narrative than M1, whose core search loop depends more heavily on physical library generation and FACS screening. M1 is retained as a comparator because it can reveal histidine-independent pH-switching solutions and therefore exposes the selected method's histidine-centered bias. M2's assay limitations are treated as a validation requirement rather than ignored: downstream planning should include an orthogonal biophysical check such as SPR on monomeric Fab where feasible to distinguish intrinsic affinity from avidity/stoichiometry effects.", |
| "uncertainty": { |
| "source_count": 2, |
| "machine_flagged_tensions": [], |
| "source_scope": "Abstract-level claim review; method records are researcher assertions.", |
| "method_references_independently_checked": false, |
| "confidence_calibrated": false, |
| "scientific_execution_verified": false, |
| "note": "Selection is a reasoned draft decision, not a probability of success or proven superiority." |
| }, |
| "evaluation_id": "00c440f3a78a95a1703725ea261b992ab51551d1dedd9cf41ba481dd0954f231" |
| } |
