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Agent skills
claude-code

Topic: claude-code

35,830 skills in this topic.

protein-qc Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite scoring. This skill provides research-backed thresholds from binder design competitions and published benchmarks.
adaptyvbio/protein-design-skills 125
proteinmpnn Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design. For backbone generation, use rfdiffusion or bindcraft. For ligand-aware design, use ligandmpnn. For solubility optimization, use solublempnn.
adaptyvbio/protein-design-skills 125
rfdiffusion Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers. For sequence design after backbone generation, use proteinmpnn. For structure validation, use alphafold or chai. For QC thresholds, use protein-qc.
adaptyvbio/protein-design-skills 125
setup First-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with "file not found" or "modal: command not found", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.
adaptyvbio/protein-design-skills 125
solublempnn Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation. For standard design, use proteinmpnn. For ligand-aware design, use ligandmpnn.
adaptyvbio/protein-design-skills 125
uniprot Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, use pdb. For sequence design, use proteinmpnn.
adaptyvbio/protein-design-skills 125
alphafold Validate protein designs using AlphaFold2 structure prediction. Use this skill when: (1) Validating designed sequences fold correctly, (2) Predicting binder-target complex structures, (3) Calculating confidence metrics (pLDDT, pTM, ipTM), (4) Self-consistency validation of designs, (5) Multi-chain complex prediction with AlphaFold-Multimer. For faster single-chain prediction, use esm. For QC thresholds, use protein-qc.
adaptyvbio/protein-design-skills 125
approach-evaluation Research industry standards and best practices, identify viable approaches for a given technical or architectural problem, and produce a structured factual comparison against project-specific constraints. Reports options — does not decide.
Fr-e-d/GAAI-framework 123
architecture-extract Convert raw project structure into clear architectural understanding — module boundaries, data flows, service relationships, and architectural patterns. Activate after codebase-scan during Bootstrap.
Fr-e-d/GAAI-framework 123
build-agents-index Scan all agent and sub-agent definition files in .gaai/core/agents/, extract YAML frontmatter, merge with specialists.registry.yaml, and generate a derived agents-index.yaml at .gaai/core/agents/agents-index.yaml. Activate after adding, modifying, or removing any agent, sub-agent, or specialist entry.
Fr-e-d/GAAI-framework 123
build-skills-index Scan SKILL.md files in .gaai/core/skills/ and .gaai/project/skills/, extract YAML frontmatter, and regenerate separate skills indices for each layer. Core index ships with the OSS framework; project index is project-specific.
Fr-e-d/GAAI-framework 123
codebase-scan Create a high-level map of the project structure and identify architectural pillars, entry points, and module boundaries. Activate at Bootstrap initialization or before architecture extraction.
Fr-e-d/GAAI-framework 123
consistency-check Detect inconsistencies across related artefacts and governance constraints. Activate after story generation, after plan preparation, before implementation, or after remediation attempts. Reports issues — does not fix them.
Fr-e-d/GAAI-framework 123
context-building Assemble a minimal, high-signal execution context bundle from already-retrieved memory, governed artefacts, and applicable rules. Activate after memory-retrieve and before any reasoning or execution skill.
Fr-e-d/GAAI-framework 123
create-skill Guide creation of a new GAAI skill following the agentskills.io spec and GAAI best practices. Activate when adding a new skill to the .gaai/core/skills/ catalog.
Fr-e-d/GAAI-framework 123
decision-extraction Identify and formalize durable product and technical decisions from agent outputs into long-term memory. Activate after Discovery produces artefacts, Delivery resolves trade-offs, or product direction materially changes.
Fr-e-d/GAAI-framework 123
delivery-readiness-audit Spot-check AC internal consistency and scan for pending revisions on delivery-ready stories. Activated by `/gaai-status --audit` as Section 5. Complements the standard status checks with depth checks that standard status skips for speed.
Fr-e-d/GAAI-framework 123
eval-run Evaluate any output file against a structured evals.yaml assertions file and produce a score report with per-assertion pass/fail results. Activate when the Discovery Agent runs the Skill Optimize protocol to measure output quality or detect regressions after skill instruction changes.
Fr-e-d/GAAI-framework 123
friction-retrospective Scan delivery artefacts for friction log entries, detect recurring patterns, and produce retrospective reports. Invoked by Discovery Agent (never by Delivery) to identify systemic improvement opportunities from friction captured during delivery.
Fr-e-d/GAAI-framework 123
i18n-glossary-sync Maintain a canonical i18n glossary file — sync new terms across all language pairs, detect drift, flag missing translations, and enforce consistent terminology across the codebase.
Fr-e-d/GAAI-framework 123
i18n-validate Validate translation completeness and consistency across all locale files — detect missing keys, untranslated strings, format mismatches, and glossary violations.
Fr-e-d/GAAI-framework 123
idiomatic-translate Translate strings idiomatically across multiple target languages using a project glossary, preserving tone, domain terminology, and format placeholders while flagging untranslatable content.
Fr-e-d/GAAI-framework 123
memory-alignment-check After QA PASS, compare the Story's implementation footprint against relevant memory entries. Reports confirmed entries, contradictions, and new knowledge candidates. Never writes to memory — produces a delta report for Discovery to action.
Fr-e-d/GAAI-framework 123
memory-compact Emergency single-pass memory compression when context window pressure is high mid-task. Activate when approaching token limits during active work. For scheduled end-of-phase cleanup, use memory-refresh instead.
Fr-e-d/GAAI-framework 123