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 boltzgen instead. For structure prediction only, use proteus-fold. For scoring and screening, use by-scoring and by-screening.
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 the user needs to design an antibody or nanobody binder against a protein target.
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 pipeline stages, (5) Setting quality thresholds and acceptance criteria, (6) Determining when to accept vs re-run designs. For detailed scoring guidance, use by-scoring. For screening specifics, use by-screening. For epitope/hotspot analysis, use by-epitope-analysis. For campaign planning and state management, use by-campaign-manager. For database queries (PDB, UniProt, SAbDab), use by-database.
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 target lookups, (5) Showing long-running job progress.
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 .by/config.json or .by/environment.json.
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, starting a new design campaign, investigating prior art, analyzing epitopes, reviewing literature for design strategy, or when the user mentions target research, literature search, or prior art in the context of protein/antibody design.
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 ensemble validation, (5) Predicting protein-ligand complexes. For design generation, use proteus-prot or boltzgen instead. For scoring existing predictions, use by-scoring. For full pipeline orchestration, use by-design-workflow.
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 approaches exist.