[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DCTY22YKDB5GR89Y9023MA":3,"skill-same:01M6DCTY22YKDB5GR89Y9023MA":53},{"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":28,"linkOnly":29,"markdownContent":30,"markdownBody":31,"frontMatter":32,"refName":33,"commitSha":34,"skillDirectory":35,"forksCount":14,"repositoryHtmlUrl":36,"repositoryHomepageUrl":6,"ownerHtmlUrl":37,"ownerBlogUrl":6,"ownerDescription":6,"updatedAt":38,"install":39,"resources":52},"01M6DCTY22YKDB5GR89Y9023MA","protein-interaction-network-analysis",null,"Use when analyzing protein interaction networks, confidence scores, functional enrichment, or structural context with STRING, BioGRID, and SASBDB.","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\u002Fprotein-interaction-network-analysis\u002FSKILL.md",[],[19,20,21,22,23,24,25,26,27],"network","analysis","protein interaction network analysis","analyzing","enrichment","networks","context","use","structural","2026-11-10 10:12:30",false,"---\nname: protein-interaction-network-analysis\ndescription: \"Use when analyzing protein interaction networks, confidence scores, functional enrichment, or structural context with STRING, BioGRID, and SASBDB.\"\n---\n\n# Protein Interaction Network Analysis\n\nComprehensive protein interaction network analysis using ToolUniverse tools. Analyzes protein networks through a 4-phase workflow: identifier mapping, network retrieval, enrichment analysis, and optional structural data.\n\n## Domain Reasoning: Interaction Type Clarification\n\nWhen asked about protein interactions, ask: physical interaction (do they bind?) or functional interaction (do they affect the same pathway)? STRING combines both — a high combined_score does not mean physical binding. For physical binding evidence, check the experimental score (`escore`) specifically. A high `tscore` (text mining) or `dscore` (database) with a low `escore` suggests co-annotation or co-citation, not direct binding.\n\nLOOK UP DON'T GUESS: protein interaction scores, experimental evidence types, and whether two specific proteins have known co-crystal structures. Use STRING `escore` and BioGRID experimental data — do not infer binding from pathway co-membership alone.\n\n## Databases Used\n\n| Database | Coverage | API Key | Purpose |\n|----------|----------|---------|---------|\n| **STRING** | 14M+ proteins, 5,000+ organisms | Not required | Primary interaction source |\n| **BioGRID** | 2.3M+ interactions, 80+ organisms | Required | Fallback, curated data |\n| **SASBDB** | 2,000+ SAXS\u002FSANS entries | Not required | Solution structures |\n\n## 4-Phase Workflow\n\n1. **Identifier Mapping** — `STRING_map_identifiers()`: validate protein names, get STRING IDs\n2. **Network Retrieval** — `STRING_get_network()` (primary); `BioGRID_get_interactions()` (fallback, requires API key)\n\n### Parameters\n### Confidence Score Guidelines\n### Network Edge Fields (STRING)\n### Extended Analysis Tools\n### Tool-Specific Notes\n### IntAct Interaction Data\n### BioGRID Chemical Interactions\n### IntAct `protein_name` Alias\n### Domain Reasoning: Multimeric Assemblies & Binding Valency\n### Calculating Multimer Valency from Binding Data\n","# Protein Interaction Network Analysis\n\nComprehensive protein interaction network analysis using ToolUniverse tools. Analyzes protein networks through a 4-phase workflow: identifier mapping, network retrieval, enrichment analysis, and optional structural data.\n\n## Domain Reasoning: Interaction Type Clarification\n\nWhen asked about protein interactions, ask: physical interaction (do they bind?) or functional interaction (do they affect the same pathway)? STRING combines both — a high combined_score does not mean physical binding. For physical binding evidence, check the experimental score (`escore`) specifically. A high `tscore` (text mining) or `dscore` (database) with a low `escore` suggests co-annotation or co-citation, not direct binding.\n\nLOOK UP DON'T GUESS: protein interaction scores, experimental evidence types, and whether two specific proteins have known co-crystal structures. Use STRING `escore` and BioGRID experimental data — do not infer binding from pathway co-membership alone.\n\n## Databases Used\n\n| Database | Coverage | API Key | Purpose |\n|----------|----------|---------|---------|\n| **STRING** | 14M+ proteins, 5,000+ organisms | Not required | Primary interaction source |\n| **BioGRID** | 2.3M+ interactions, 80+ organisms | Required | Fallback, curated data |\n| **SASBDB** | 2,000+ SAXS\u002FSANS entries | Not required | Solution structures |\n\n## 4-Phase Workflow\n\n1. **Identifier Mapping** — `STRING_map_identifiers()`: validate protein names, get STRING IDs\n2. **Network Retrieval** — `STRING_get_network()` (primary); `BioGRID_get_interactions()` (fallback, requires API key)\n\n### Parameters\n### Confidence Score Guidelines\n### Network Edge Fields (STRING)\n### Extended Analysis Tools\n### Tool-Specific Notes\n### IntAct Interaction Data\n### BioGRID Chemical Interactions\n### IntAct `protein_name` Alias\n### Domain Reasoning: Multimeric Assemblies & Binding Valency\n### Calculating Multimer Valency from Binding Data\n",{"name":5,"description":7},"main","a298c929b6cbd662e1fce54302ce520d5ceea1a5","platform\u002Frouting\u002Ffixtures\u002Fhome\u002F.agents\u002Fskills\u002Fprotein-interaction-network-analysis","https:\u002F\u002Fgithub.com\u002FPrekzursil\u002Fagent-skills-toolchain","https:\u002F\u002Fgithub.com\u002FPrekzursil","2026-11-02 14:30:57",{"source":8,"skillName":5,"commands":40,"prompt":50,"zipAvailable":51},[41,44,47],{"tool":42,"command":43},"npx","npx skills add Prekzursil\u002Fagent-skills-toolchain --skill protein-interaction-network-analysis",{"tool":45,"command":46},"bunx","bunx skills add Prekzursil\u002Fagent-skills-toolchain --skill protein-interaction-network-analysis",{"tool":48,"command":49},"pnpm","pnpm dlx skills add Prekzursil\u002Fagent-skills-toolchain --skill protein-interaction-network-analysis","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\u002Fprotein-interaction-network-analysis\u002FSKILL.md",true,[],[54,74,105,132,146,162],{"skillNo":55,"name":56,"nameZh":6,"description":57,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":58,"categories":59,"keywords":60,"publishedAt":28},"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",[],[61,62,63,64,65,66,67,68,69,26,25,70,71,72,73],"clarify requirements","clarify","requirements","risk","options","task","prompts","goal","scanning","repo","injection","execution","file",{"skillNo":75,"name":76,"nameZh":6,"description":77,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":78,"categories":79,"keywords":85,"publishedAt":28},"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",[80],{"categoryNo":81,"categoryName":82,"taxonomyType":83,"taxonomyTypeDesc":84},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[86,87,88,89,90,91,92,93,94,95,96,97,98,99,26,100,101,102,103,104],"openmm md","how","decision","pick","linux","analyze","tool","stack","open","NVIDIA","gpu","license","workflow","windows","free","molecular dynamics","local","do","MCP",{"skillNo":106,"name":107,"nameZh":6,"description":108,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":109,"categories":110,"keywords":117,"publishedAt":28},"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",[111,114],{"categoryNo":112,"categoryName":113,"taxonomyType":83,"taxonomyTypeDesc":84},"01JBSEEDCAT000000000000003","演示文稿",{"categoryNo":115,"categoryName":116,"taxonomyType":83,"taxonomyTypeDesc":84},"01JBSEEDCAT000000000000008","测试与质量",[118,119,120,121,122,123,124,125,126,127,87,128,129,130,131],"review","visual","visual review","pages","web","false","iteration","take","check","slides","ui","screenshot","playwright","screenshots",{"skillNo":133,"name":134,"nameZh":6,"description":135,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":136,"categories":137,"keywords":138,"publishedAt":28},"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",[],[134,139,140,141,142,143,144,145],"setup","report","project","installation","project setup","issues","state",{"skillNo":147,"name":148,"nameZh":6,"description":149,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":150,"categories":151,"keywords":153,"publishedAt":28},"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",[152],{"categoryNo":81,"categoryName":82,"taxonomyType":83,"taxonomyTypeDesc":84},[148,154,66,155,156,157,26,158,159,160,161],"start issue","issue","ready","work on issue","user","work","work on","development",{"skillNo":163,"name":139,"nameZh":6,"description":164,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":165,"categories":166,"keywords":167,"publishedAt":28},"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",[],[139,141,102,168,143,169],"files","interactive"]