AI-powered biologics design campaign agent — multi-agent orchestration with BoltzGen, PXDesign, Protenix, and 200+ cloud tools. Antibodies, nanobodies, de novo binders, and beyond.
Skill Claude CodeCodex
BoltzGen is an all-atom diffusion model that generates antibody, nanobody, and de novo miniprotein backbones conditioned on a target structure and a set of binding (hotspot) residues. Sequences are assigned by AntiFold, then each design is independently refolded with Protenix to produce ipTM, pTM, pLDDT, ipSAE, and…
Skill Claude CodeCodex
Plan, execute, monitor, and assess protein/antibody design campaigns. This skill governs how to size a campaign, track run state, coordinate multi-run efforts, estimate cost and time on each compute target (local GPU, HPC, Tamarind), monitor progress, and evaluate campaign health.
Skill Claude CodeCodex
Multi-round design campaigns generate scored designs at every iteration. This skill turns that scoring history into actionable parameter changes for the next round — training a lightweight Random Forest on the designs you already have, ranking which features actually discriminate good from bad, and proposing…
Skill Claude CodeCodex
Most "AI scientist" demos fake reasoning by chaining LLM calls and calling the chain a hypothesis. This skill does the opposite: it constrains the LLM with structured evidence retrieved from the BY knowledge graph and forces every claim to cite an existing entity with a defined evidence tier. The output is a short…
Skill Claude CodeCodex
Use the BY MCP database tools to query PDB, UniProt, and SAbDab for target characterization, antibody scaffold selection, and competition analysis.
Skill Claude CodeCodex
BY is a local-first agent. The default compute provider is "local" (see .by/config.json → compute.defaultprovider). This skill teaches you how to stand up each design and folding tool on hardware the user owns or pays for directly — a personal GPU workstation, a RunPod pod, a Modal app, or a generic SLURM/PBS cluster…
Skill Claude CodeCodex
Skill "by-design-workflow" from 001TMF/blatant-why, covering by design workflow — master orchestration skill, when to use this skill, inputs, outputs and clarification questions.
Skill Claude CodeCodex
Standard display formats for all campaign output. They use Unicode box-drawing characters and markdown that render natively in Claude Code's terminal. Never use ANSI escape codes in response text — they render as literal characters.
Skill Claude CodeCodex
You are an expert structural biologist performing epitope analysis and hotspot residue selection for protein and antibody binder design. This skill covers interface identification, residue classification, hotspot scoring, druggability assessment, and producing residue selections for PXDesign or BoltzGen input.
Skill Claude CodeCodex
A design campaign only learns when lab outcomes are joined back to the in-silico predictions that produced them. This skill is the wet-lab feedback loop closer: it ingests lab readouts (Adaptyv batch CSVs, internal ELISA plate-reader output, BLI/Octet kinetics, expression QC), joins them to the per-design feature…
Skill Claude CodeCodex
Closing the design feedback loop requires understanding why designs fail, not just that they fail. This skill compares the distribution of every continuous feature between PASS and FAIL designs using non-parametric statistics, ranks features by discriminating power, and translates the result into concrete threshold or…
Skill Claude CodeCodex
Picking the wrong design strategy on a novel target wastes a GPU day. This skill forces an explicit, structured debate before any compute is spent: three hypothesis agents propose competing strategies in parallel, then a reflection agent ranks them against a fixed rubric. The winner becomes the campaign config.
Skill Claude CodeCodex
Persistent structured memory that turns isolated campaigns into a learning system. Each campaign writes outcomes, top designs, and failure modes into a JSON-backed graph so the next campaign benefits from prior art without re-running compute.
Skill Claude CodeCodex
Thorough target research before design prevents wasted compute and failed campaigns. This skill defines an 8-phase pipeline that retrieves, validates, and packages research findings with quality gates and anti-drift checkpoints at every stage.
Skill Claude CodeCodex
Interpret and apply BY custom scoring metrics for protein and antibody design. This skill covers ipSAE (interface Predicted Structural Accuracy Error) — the primary custom metric that differentiates BY from generic structure prediction tools — along with ipTM, pLDDT, RMSD, liability scoring, and the BY composite…
Skill Claude CodeCodex
Comprehensive screening battery for evaluating protein binder and antibody designs produced by PXDesign and BoltzGen. This skill encodes all quality filters, scoring thresholds, liability checks, and developability assessments used to triage designs before experimental validation.
Skill Claude CodeCodex
Session initialization and configuration for BY projects. This skill defines the full session-start sequence (banner, environment check, status display) and the first-run configuration questionnaire that writes .by/config.json. It is not optional — it runs every time a new session opens in a BY project directory.
Skill Claude CodeCodex
Protenix v1 is an AF3-class structure prediction model (368M parameters) for proteins, complexes, and protein-ligand systems. This skill wraps the protenix CLI with a documented input spec, an input-validating Python entry point, and a multi-seed ensemble aggregator so that callers can drive predictions through…
Skill Claude CodeCodex
You are an expert at designing de novo protein binders using PXDesign. This skill covers YAML config construction, CLI invocation, output parsing, and result interpretation. PXDesign achieves 17–82% pass rate for de novo binder design depending on target difficulty (see references/de-novo-strategy.md).
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: