001TMF/blatant-why

001TMF/blatant-why

Agent Claude Code

Plan design campaigns. Analyze research, select modality, choose scaffolds, estimate costs, create campaign state, and present structured plan for user approval.

001TMF/blatant-why

Agent Claude Code

Generate protein/antibody designs using available compute providers (Tamarind, local GPU). Creates tool inputs, submits jobs, and monitors progress.

001TMF/blatant-why

Agent Claude Code

Analyze sequence and structural diversity across a design set. Sequence clustering, structural clustering, Pareto front analysis, scaffold balance, phylogenetic dendrograms, and diverse panel selection.

001TMF/blatant-why

Agent Claude Code

Discover available tools, compute providers, GPU access, API keys, and configuration. Produces structured environment.json for use by all other agents.

001TMF/blatant-why

Agent Claude Code

Parallel epitope surface analysis. Identifies druggable sites, hotspot residues, scores epitope accessibility and druggability. Lighter-weight than the full by-epitope agent.

001TMF/blatant-why

Agent Claude Code

Deep epitope analysis agent. Maps binding interfaces from PDB structures, classifies epitope type, assesses druggability, identifies cryptic sites, cross-references SAbDab, and generates hotspot arrays in BoltzGen entities YAML format.

001TMF/blatant-why

Agent Claude Code

Independent structural evaluation of designs. Deep structural analysis including refolding validation, interface quality, comparison to known binders, confidence decomposition, aggregation risk, and cross-validation.

001TMF/blatant-why

Agent Claude Code

Format designs for downstream use. scFv conversion, Fab assembly, expression vector design, codon optimization hints, multi-format output (FASTA/GenBank/entities YAML), and Adaptyv Bio submission formatting.

001TMF/blatant-why

Agent Claude Code

Humanize non-human antibody sequences for therapeutic development. Framework analysis, CDR grafting onto human germlines, back-mutation identification, T-cell epitope prediction, humanness scoring, and humanized variant panel generation.

001TMF/blatant-why

Agent Claude Code

Query and update the learning system. Store campaign outcomes, query similar campaigns, get scaffold rankings, record failures, and generate recommendations.

001TMF/blatant-why

Agent Claude Code

Handle Adaptyv Bio lab submissions with triple safety gate. Presents cost estimates, validates approval chain, and submits only when all three gates pass.

001TMF/blatant-why

Agent Claude Code

Actively propose mutations to fix identified sequence liabilities. Score mutations for structural impact, consider framework vs CDR context, generate ranked mutation panels with predicted impact, and output mutation tables with position, original, proposed, motif removed, and risk level.

001TMF/blatant-why

Agent Claude Code

Review campaign plans for completeness and correctness before user approval. Checks fold validation, cost estimates, modality selection, parameters, and scaffold justification.

001TMF/blatant-why

Agent Claude Code

Parallel prior art research via SAbDab, PubMed, bioRxiv, and literature. Finds existing binders, antibodies, nanobodies against the target. Maps the competitive landscape.

001TMF/blatant-why

Agent Claude Code

Synthesizes outputs from 4 parallel research agents into a unified target report. Reads targetstructures.json, targetsequence.json, priorart.json, and epitopeanalysis.json. Produces targetreport.json and researchreport.md.

001TMF/blatant-why

Agent Claude Code

Target analysis, literature review, prior art search, epitope identification using PDB, UniProt, SAbDab, and research MCP tools.

001TMF/blatant-why

Agent Claude Code

Score, filter, and rank designs. Run liability screening, developability checks, and composite scoring (ipSAE, ipTM, pLDDT). Present ranked candidates.

001TMF/blatant-why

Agent Claude Code

Parallel target sequence research via UniProt. Identifies canonical sequence, domains, PTMs, variants, functional regions, and druggability indicators.

001TMF/blatant-why

Agent Claude Code

Parallel target structure research via PDB. Finds best resolution crystal structures, identifies chains, interfaces, binding surfaces, and downloads the optimal structure for design.

001TMF/blatant-why

Agent Claude Code

Independent quality gate checker. Verifies structural metrics, screening completeness, and candidate integrity before results are presented to the user.

001TMF/blatant-why

Agent Claude Code

Generate PyMOL and ChimeraX session scripts for structural visualization. Creates publication-quality views of targets, designed complexes, interfaces, CDR loops, electrostatic surfaces, and clash detection.