[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DCFMFC49RMCCME8SG6EKM4":3,"skill-same:01M6DCFMFC49RMCCME8SG6EKM4":64},{"skillNo":4,"name":5,"nameZh":6,"description":7,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":16,"categories":17,"keywords":18,"publishedAt":39,"linkOnly":40,"markdownContent":41,"markdownBody":42,"frontMatter":43,"refName":44,"commitSha":45,"skillDirectory":46,"forksCount":14,"repositoryHtmlUrl":47,"repositoryHomepageUrl":6,"ownerHtmlUrl":48,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":49,"install":50,"resources":63},"01M6DCFMFC49RMCCME8SG6EKM4","comp-pharm-cascade",null,"Use when ranking\u002Fprioritizing a congeneric small-molecule series against a protein target (binding-affinity SAR, hit triage, mechanism-of-action), or when scoping such a campaign. Routes the work through a cost-escalating cascade — experimental-anchor data → license-free ML (Boltz-2) breadth + pose → licensed Schrödinger physics (FEP\u002FMM-GBSA\u002FBPMD) for the headline ΔΔG → QM (EXESS) mechanism → figures — with consensus checks at the two gates that are catastrophic when silently wrong (pose, and the published number). NOT for a single one-off docking (use schrodinger-maestro-driver \u002F structure-based-screening) or pure knowledge lookup (use tooluniverse).","Prekzursil\u002Fagent-skills-toolchain","Prekzursil","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F54636077?v=4","01M6DACZ1PCQHD99SCR1YXG28B","Andrei Mihai Visalon","01M6DACZ670WZF535V3WYYSS4Z",0,"MIT","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Fplatform\u002Frouting\u002Ffixtures\u002Fhome\u002F.agents\u002Fskills\u002Fcomp-pharm-cascade\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],"comp pharm cascade","structure","tooluniverse","free","gates","schrödinger","series","docking","anchor","physics","triage","cost","campaign","use","consensus","work","knowledge","data","license","ml","2026-11-10 10:12:30",false,"---\nname: comp-pharm-cascade\ndescription: >-\n  Use when ranking\u002Fprioritizing a congeneric small-molecule series against a\n  protein target (binding-affinity SAR, hit triage, mechanism-of-action), or\n  when scoping such a campaign. Routes the work through a cost-escalating\n  cascade — experimental-anchor data → license-free ML (Boltz-2) breadth +\n  pose → licensed Schrödinger physics (FEP\u002FMM-GBSA\u002FBPMD) for the headline\n  ΔΔG → QM (EXESS) mechanism → figures — with consensus checks at the two\n  gates that are catastrophic when silently wrong (pose, and the published\n  number). NOT for a single one-off docking (use schrodinger-maestro-driver \u002F\n  structure-based-screening) or pure knowledge lookup (use tooluniverse).\n---\n\n# comp-pharm-cascade\n\nOrchestration skill: how a target + ligand series flows through the available\ncompute stack to a defensible affinity\u002Fmechanism result. This is a **routing\nlaw over executor skills**, not a new engine. Reference implementation: the\nphenibut α2δ-1 \u002F GABA_B campaign (worked numbers at the bottom).\n\n## Core principle — a cascade with two guarded gates\n\nEscalate cost only when the cheaper tier can't answer. But a naive cascade is\n**brittle where campaigns actually break**: it trusts each tier and escalates\nupward, so a wrong pose makes MM-GBSA, FEP, and QM all rank garbage *equally*.\nSo spend redundancy surgically at the **two checkpoints where being wrong is\ncatastrophic and silent**, single-track everywhere else.\n\n- **Gate 1 — Pose.** A pose is trusted only when independent methods agree\n  (Boltz-2 co-fold ipTM\u002FPAE ∩ Glide\u002FIFD ∩ BPMD stability). Cheap ensemble at\n  the known failure point. Never rescore an unvalidated pose.\n- **Gate 2 — The published number.** The one headline ΔΔG gets FEP **plus** one\n  orthogonal corroborator (Boltz affinity *or* QM decomposition) **plus** the\n  experimental value. Everything else in the SAR runs single-method, flagged\n  lower-confidence.\n\n## Tier map (cheap → expensive)\n\n| Tier | Capability | Executor | Note |\n|------|-----------|----------|------|\n| **0 — Anchor** ⭐ | Experimental Ki\u002FIC50\u002FEC50, the y-axis | ChEMBL MCP \u002F GtoPdb \u002F `tooluniverse` pharmacology | **Run FIRST.** No ground truth → no rankable claim (see Gate 0). |\n\n### Canonical phase pipeline\n### Substrate & ops (hard-won)\n### Worked reference — phenibut (2026-07-04)\n","# comp-pharm-cascade\n\nOrchestration skill: how a target + ligand series flows through the available\ncompute stack to a defensible affinity\u002Fmechanism result. This is a **routing\nlaw over executor skills**, not a new engine. Reference implementation: the\nphenibut α2δ-1 \u002F GABA_B campaign (worked numbers at the bottom).\n\n## Core principle — a cascade with two guarded gates\n\nEscalate cost only when the cheaper tier can't answer. But a naive cascade is\n**brittle where campaigns actually break**: it trusts each tier and escalates\nupward, so a wrong pose makes MM-GBSA, FEP, and QM all rank garbage *equally*.\nSo spend redundancy surgically at the **two checkpoints where being wrong is\ncatastrophic and silent**, single-track everywhere else.\n\n- **Gate 1 — Pose.** A pose is trusted only when independent methods agree\n  (Boltz-2 co-fold ipTM\u002FPAE ∩ Glide\u002FIFD ∩ BPMD stability). Cheap ensemble at\n  the known failure point. Never rescore an unvalidated pose.\n- **Gate 2 — The published number.** The one headline ΔΔG gets FEP **plus** one\n  orthogonal corroborator (Boltz affinity *or* QM decomposition) **plus** the\n  experimental value. Everything else in the SAR runs single-method, flagged\n  lower-confidence.\n\n## Tier map (cheap → expensive)\n\n| Tier | Capability | Executor | Note |\n|------|-----------|----------|------|\n| **0 — Anchor** ⭐ | Experimental Ki\u002FIC50\u002FEC50, the y-axis | ChEMBL MCP \u002F GtoPdb \u002F `tooluniverse` pharmacology | **Run FIRST.** No ground truth → no rankable claim (see Gate 0). |\n\n### Canonical phase pipeline\n### Substrate & ops (hard-won)\n### Worked reference — phenibut (2026-07-04)\n",{"name":5,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5","platform\u002Frouting\u002Ffixtures\u002Fhome\u002F.agents\u002Fskills\u002Fcomp-pharm-cascade","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 14:30:57",{"source":8,"skillName":5,"commands":51,"prompt":61,"zipAvailable":62},[52,55,58],{"tool":53,"command":54},"npx","npx skills add Prekzursil\u002Fagent-skills-toolchain --skill comp-pharm-cascade",{"tool":56,"command":57},"bunx","bunx skills add Prekzursil\u002Fagent-skills-toolchain --skill comp-pharm-cascade",{"tool":59,"command":60},"pnpm","pnpm dlx skills add Prekzursil\u002Fagent-skills-toolchain --skill comp-pharm-cascade","安装技能，技能地址：https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Fplatform\u002Frouting\u002Ffixtures\u002Fhome\u002F.agents\u002Fskills\u002Fcomp-pharm-cascade\u002FSKILL.md",true,[],[65,86,115,142,156,171],{"skillNo":66,"name":67,"nameZh":6,"description":68,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":69,"categories":70,"keywords":71,"publishedAt":39},"01M6DF7D7478R55P46REYH4QAC","clarify-requirements","Resolve genuine pre-execution ambiguity by scanning repo context, generating 1-6 grounded options, and asking 1-3 focused questions via AskUserQuestion. NOT for mid-task use (injection risk); NOT when the goal is already unambiguous; use to disambiguate vague prompts before any file edits.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fworkspace-hooks\u002Fskills\u002Fclarify-requirements\u002FSKILL.md",[],[72,73,74,75,76,77,78,79,80,32,81,82,83,84,85],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","context","repo","injection","execution","file",{"skillNo":87,"name":88,"nameZh":6,"description":89,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":90,"categories":91,"keywords":97,"publishedAt":39},"01M6DF79CA4BHJS66J8EZDBPWJ","openmm-md","Run FREE, open-source, Windows-native GPU molecular dynamics via the openmm-md MCP (OpenMM + CUDA on the local NVIDIA GPU). Use for protein \u002F protein-ligand MD when you want a free stack or are on Windows without a Schrodinger license. Covers the full workflow (prepare, solvate, minimize, equilibrate, production, analyze, mmgbsa) AND an honest decision guide vs Schrodinger Desmond, including how to run Desmond legitimately on Linux or a cloud GPU with a real license. This is a deliberately LESSER free alternative and does NOT replace the schrodinger MCP tools. Do NOT use it to pick a free tool when a validated FEP+, WaterMap, IFD-MD, or Prime MM-GBSA result is actually required.","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Fmcp\u002Fopenmm-md-mcp\u002Fskill\u002Fopenmm-md\u002FSKILL.md",[92],{"categoryNo":93,"categoryName":94,"taxonomyType":95,"taxonomyTypeDesc":96},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[98,99,100,101,102,103,104,105,106,107,108,37,109,110,32,22,111,112,113,114],"openmm md","how","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","workflow","windows","molecular dynamics","local","do","MCP",{"skillNo":116,"name":117,"nameZh":6,"description":118,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":119,"categories":120,"keywords":127,"publishedAt":39},"01M6DF76C1MG85VEWP8VZCBNMN","visual-review","Take screenshots of web pages and UI using Playwright for visual review and iteration","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fvisual-review\u002FSKILL.md",[121,124],{"categoryNo":122,"categoryName":123,"taxonomyType":95,"taxonomyTypeDesc":96},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":125,"categoryName":126,"taxonomyType":95,"taxonomyTypeDesc":96},"01JBSEEDCAT000000000000008","测试与质量",[128,129,130,131,132,133,134,135,136,137,99,138,139,140,141],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":143,"name":144,"nameZh":6,"description":145,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":146,"categories":147,"keywords":148,"publishedAt":39},"01M6DF73AQVCBZKEN0YXEX9FXP","status","Diagnostic status report — shows metaswarm installation state, project setup, and potential issues","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstatus\u002FSKILL.md",[],[144,149,150,151,152,153,154,155],"setup","report","project","installation","project setup","issues","state",{"skillNo":157,"name":158,"nameZh":6,"description":159,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":160,"categories":161,"keywords":163,"publishedAt":39},"01M6DF6X6C2XB0P6GX76P7TTYV","start","Use when starting work on any task, when the user mentions metaswarm, or when the user wants to begin tracked development work","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fstart\u002FSKILL.md",[162],{"categoryNo":93,"categoryName":94,"taxonomyType":95,"taxonomyTypeDesc":96},[158,164,77,165,166,167,32,168,34,169,170],"start issue","issue","ready","work on issue","user","work on","development",{"skillNo":172,"name":149,"nameZh":6,"description":173,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":174,"categories":175,"keywords":176,"publishedAt":39},"01M6DF6QMJ9AJKFKHHKRT005PQ","Interactive project setup — detects your project, configures metaswarm, writes project-local files","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain\u002Fblob\u002Fmain\u002Ftools\u002Feditor\u002Fmetaswarm\u002Fskills\u002Fsetup\u002FSKILL.md",[],[149,151,112,177,153,178],"files","interactive"]