001TMF

001TMF/blatant-why

Command Claude Code

Show ranked design results.

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Command Claude Code

Run full screening battery on a design.

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Command Claude Code

Show current campaign status.

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Command Claude Code

Watch live pipeline progress for a design run.

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Settings file Claude Code

MCP configuration declaring 11 servers: by-pdb, by-uniprot, by-sabdab, by-tamarind, by-cloud, by-adaptyv.

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Instructions file

Instructions for 001TMF/blatant-why, covering claude.md — by (blatant-why) dev context, about this file, dev guidelines, git workflow and review checklist.

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Agent Claude Code

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

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Agent Claude Code

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

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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.

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Agent Claude Code

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

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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.

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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.

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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.

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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.

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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.

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Agent Claude Code

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

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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.

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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.

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Agent Claude Code

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

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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.

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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.

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Agent Claude Code

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

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Agent Claude Code

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

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Agent Claude Code

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