001tmf/blatant-why
19 skills
$npx skills add 001tmf/blatant-whySkillInstalls
boltzgenBoltzGen is an all-atom diffusion model that generates antibody, nanobody, and de novo miniprotein backbones conditioned on a target structure and a set of…by-campaign-managerPlan, execute, monitor, and assess protein/antibody design campaigns.by-campaign-optimizerMulti-round design campaigns generate scored designs at every iteration.by-causal-reasoningMost "AI scientist" demos fake reasoning by chaining LLM calls and calling the chain a hypothesis.by-databaseUse the BY MCP database tools to query PDB, UniProt, and SAbDab for target characterization, antibody scaffold selection, and competition analysis.by-deploy-computeBY is a local-first agent. The default compute provider is "local" (see .by/config.json → compute.defaultprovider).by-design-workflowby-design-workflow is the routing brain of BY. It does not run any engine itself. Instead, it answers four questions before any GPU compute is committed:by-displayStandard display formats for all campaign output. They use Unicode box-drawing characters and markdown that render natively in Claude Code's terminal.by-epitope-analysisYou are an expert structural biologist performing epitope analysis and hotspot residue selection for protein and antibody binder design.by-experiment-resultsA design campaign only learns when lab outcomes are joined back to the in-silico predictions that produced them.by-failure-diagnosisClosing the design feedback loop requires understanding why designs fail, not just that they fail.by-hypothesis-debatePicking the wrong design strategy on a novel target wastes a GPU day.by-knowledgePersistent structured memory that turns isolated campaigns into a learning system.by-researchThorough target research before design prevents wasted compute and failed campaigns.by-scoringInterpret and apply BY custom scoring metrics for protein and antibody design.by-screeningComprehensive screening battery for evaluating protein binder and antibody designs produced by PXDesign and BoltzGen.by-sessionSession initialization and configuration for BY projects. This skill defines the full session-start sequence (banner, environment check, status display) and…protenixProtenix v1 is an AF3-class structure prediction model (368M parameters) for proteins, complexes, and protein-ligand systems.pxdesignYou are an expert at designing de novo protein binders using PXDesign.