001TMF

De novo protein binder design using PXDesign. Use this skill when designing non-antibody protein binders against a target structure. Covers YAML config creation, CLI invocation, output parsing, and result interpretation. For antibody/nanobody binders, use…

Antibody and nanobody binder design using BoltzGen (BoltzGen diffusion + Protenix refolding). Covers entity YAML specification, CLI invocation, protocol selection (nanobody-anything / antibody-anything), MSA modes, and output parsing. Use this skill whenever…

Master orchestration skill for the BY protein design agent. Use this skill when: (1) Starting any new protein or antibody design project, (2) Deciding which BY tool to use for a given task, (3) Planning a design campaign end-to-end, (4) Understanding the…

Standard display formats and conversational patterns for BY output. Use this skill when: (1) Presenting campaign status, progress, or results, (2) Formatting screening reports, (3) Displaying error messages or checkpoints, (4) Presenting research findings or…

Session initialization and configuration for BY projects. Use this skill when: (1) Opening a new session in a BY project directory, (2) Running first-time setup (config questionnaire), (3) Checking environment and compute availability, (4) Reading or updating…

Deep academic research for antibody design campaigns — target analysis, literature review, prior art search, epitope identification. Uses an 8-phase pipeline with quality gates and persistent memory. Use this skill whenever researching a protein target,…

Structure prediction using Protenix v1 (AF3-class, 368M params). Use this skill when: (1) Predicting protein or complex structure from sequence, (2) Validating designed binders by refolding, (3) Generating confidence metrics (ipTM, pTM, pLDDT), (4) Multi-seed…

Hypothesis-debate pattern for design strategy selection. Spawns competing strategy agents and uses adversarial ranking to select the best approach before committing GPU compute. Use when starting a new campaign, facing a novel target, or when multiple viable…

Run a Meta-Harness-style optimization loop NATIVELY — automatically search over the scaffolding around a FIXED base model (memory, retrieval, context construction, prompt templates, summarization, tool-selection logic) by proposing candidate variants, scoring…

Run one iteration of proteus memory-summary evolution. Called by meta_harness.py.

Render and display protein structures with ProteinView FullHD pixel graphics. Use whenever a user asks to show, view, visualize, inspect, or render a Protein Data Bank/PDB identifier (for example, "show me 1UBQ PDB protein") or a local .pdb/.cif/.mmcif…

Retrieve reproducible, complete, verifiable records from 26 public biomedical sources (PDB, UniProt, NCBI Protein/Virus/Datasets, ClinVar, Ensembl, gnomAD, PubChem, AlphaFold, ClinicalTrials, openFDA, Open Targets, Reactome, GTEx, GWAS Catalog, and more — run…

Create and operate Radio rooms of named cross-harness @personas. Use when the user asks to delegate work to Claude Code, Codex, OMP, Pi, or DeepSeek agents; arrange who may communicate; send compact requests; or wait for correlated replies.