[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DMK35BHFH5TR2MEAVEDRJB":3,"skill-same:01M6DMK35BHFH5TR2MEAVEDRJB":118},{"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":23,"publishedAt":31,"linkOnly":32,"markdownContent":33,"markdownBody":34,"frontMatter":35,"refName":42,"commitSha":43,"skillDirectory":44,"forksCount":45,"repositoryHtmlUrl":46,"repositoryHomepageUrl":6,"ownerHtmlUrl":47,"ownerBlogUrl":6,"ownerDescription":48,"updatedAt":49,"install":50,"resources":63},"01M6DMK35BHFH5TR2MEAVEDRJB","peptide-properties-calculation",null,"Calculate peptide sequence properties including molecular weight, isoelectric point, extinction coefficient, and chemical formula.","InternScience\u002FDrClaw","InternScience","https:\u002F\u002Favatars.githubusercontent.com\u002Fu\u002F154449623?v=4","01M6DHY1ZF02QASNAVMNPT7NP6","Intern Science","01M6DHY2523FY56Q5572NKAAD0",172,"MIT","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fscience\u002Fprotein\u002Fpeptide-properties-calculation\u002FSKILL.md",[18],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000023","Skill与智能体开发","SCENARIO","使用场景",[24,25,26,27,28,29,30],"properties","peptide properties calculation","计算","calculate","formula","chemical","molecular","2026-11-10 10:12:30",false,"---\nname: peptide-properties-calculation\ndescription: Calculate peptide sequence properties including molecular weight, isoelectric\n  point, extinction coefficient, and chemical formula.\nlicense: MIT license\nmetadata:\n  skill-author: PJLab\ni18n:\n  zh:\n    description: 计算肽序列理化性质。\n---\n\n# Peptide Properties Calculation\n\n## Usage\n\n### 1. MCP Server Definition\n\nUse the same `BiologyToolsClient` class as defined in the protein-properties-calculation skill.\n\n### 2. Peptide Properties Calculation Workflow\n\nThis workflow calculates comprehensive physicochemical properties of peptide sequences for peptide drug design, synthesis planning, and characterization.\n\n**Workflow Steps:**\n\n1. **Calculate Peptide Properties** - Compute MW, pI, extinction coefficient, GRAVY, and chemical formula\n2. **Analyze Multiple Peptides** - Compare properties across different sequences\n\n**Implementation:**\n\n```python\n## Initialize client\nHEADERS = {\"SCP-HUB-API-KEY\": \"\u003Cyour-api-key>\"}\n\nclient = BiologyToolsClient(\n    \"https:\u002F\u002Fscp.intern-ai.org.cn\u002Fapi\u002Fv1\u002Fmcp\u002F29\u002FSciToolAgent-Bio\",\n    HEADERS\n)\n\nif not await client.connect():\n    print(\"connection failed\")\n    exit()\n\nprint(\"=== Peptide Properties Calculation ===\\n\")\n\n## Input: Peptide sequences to analyze\npeptides = [\n    (\"All 20 amino acids\", \"ACDEFGHIKLMNPQRSTVWY\"),\n    (\"Glycine repeat\", \"GGGGG\"),\n    (\"Arginine repeat (positively charged)\", \"RRRRR\"),\n]\n\n## Calculate properties for each peptide\nfor name, peptide in peptides:\n    print(f\"--- {name}: {peptide} ---\")\n\n    # Calculate peptide properties\n    result = await client.client.call_tool(\n        \"CalculatorPeptideProperty\",\n        arguments={\n            \"sq\": peptide,\n            \"aaCode\": \"0\",          # Use single-letter code\n            \"nTerm\": \"\",            # N-terminal modification (if any)\n            \"cTerm\": \"\",            # C-terminal modification (if any)\n            \"disulphideBonds\": \"\"   # Disulfide bonds (if any)\n        }\n    )\n    result_data = client.parse_result(result)\n    print(f\"{result_data}\\n\")\n\n## Additional analysis: Peptide weight calculation\nprint(\"=== Peptide Weight Calculation (Alternative Method) ===\\n\")\ntest_peptide = \"ACDEFGHIKLMNPQRSTVWY\"\n\nresult = await client.client.call_tool(\n    \"PeptideWeightCalculator\",\n    arguments={\"sequence\": test_peptide}\n)\nresult_data = client.parse_result(result)\nprint(f\"Peptide: {test_peptide}\")\nprint(f\"{result_data}\\n\")\n\n## Additional analysis: Peptide formula calculation\nprint(\"=== Peptide Chemical Formula ===\\n\")\n\nresult = await client.client.call_tool(\n    \"PeptideFormulaCalculator\",\n    arguments={\"sequence\": test_peptide}\n)\nresult_data = client.parse_result(result)\nprint(f\"Peptide: {test_peptide}\")\nprint(f\"{result_data}\\n\")\n\nawait client.disconnect()\n```\n\n### Tool Descriptions\n\n**SciToolAgent-Bio Server:**\n- `CalculatorPeptideProperty`: Calculate comprehensive peptide properties\n  - Args:\n    - `sq` (str): Peptide sequence (single or three-letter code)\n    - `aaCode` (str): \"0\" for single-letter, \"1\" for three-letter code\n    - `nTerm` (str): N-terminal modification (e.g., \"Acetyl\", \"\")\n    - `cTerm` (str): C-terminal modification (e.g., \"Amide\", \"\")\n    - `disulphideBonds` (str): Disulfide bonds specification\n  - Returns: MW, extinction coefficient, pI, GRAVY, chemical formula, sequence length\n\n- `PeptideWeightCalculator`: Calculate peptide molecular weight\n  - Args: `sequence` (str) - Peptide sequence\n  - Returns: Molecular weight in Daltons\n\n- `PeptideFormulaCalculator`: Calculate peptide chemical formula\n  - Args: `sequence` (str) - Peptide sequence\n  - Returns: Molecular formula (e.g., C₁₀₇H₁₅₉N₂₉O₃₀S₂)\n\n### Input\u002FOutput\n\n**Input:**\n- `sq`: Peptide sequence in single-letter (ACDEFG...) or three-letter (Ala-Cys-Asp...) code\n- `aaCode`: \"0\" for single-letter code, \"1\" for three-letter code\n- `nTerm`: Optional N-terminal modification\n- `cTerm`: Optional C-terminal modification\n- `disulphideBonds`: Optional disulfide bond specification\n\n**Output:**\n- **Average Molecular Weight**: Mass in g\u002Fmol or Daltons\n- **Extinction Coefficient**: For peptide quantification at 280nm (M⁻¹cm⁻¹)\n- **Theoretical Isoelectric Point (pI)**: pH at which peptide has no net charge\n- **GRAVY (Grand Average of Hydropathy)**: Hydrophobicity index\n- **Chemical Formula**: Elemental composition (C, H, N, O, S)\n- **Sequence Length**: Number of amino acid residues\n- **Three-letter Representation**: Full peptide notation\n\n### Use Cases\n\n- Design peptide drugs and therapeutics\n- Plan peptide synthesis strategies\n- Calculate peptide concentrations spectrophotometrically\n- Predict peptide solubility and stability\n- Optimize peptide purification conditions\n- Design peptide-based biosensors\n- Analyze peptide fragments from mass spectrometry\n\n### Terminal Modifications\n\nCommon N-terminal modifications:\n- **Acetyl**: Blocks N-terminus, increases stability\n- **Formyl**: Common in bacterial proteins\n- **None**: Free amine group (default)\n\nCommon C-terminal modifications:\n- **Amide**: Blocks C-terminus, increases stability\n- **None**: Free carboxyl group (default)\n\nExample with modifications:\n```python\nresult = await client.client.call_tool(\n    \"CalculatorPeptideProperty\",\n    arguments={\n        \"sq\": \"ACDEFG\",\n        \"aaCode\": \"0\",\n        \"nTerm\": \"Acetyl\",\n        \"cTerm\": \"Amide\",\n        \"disulphideBonds\": \"\"\n    }\n)\n```\n\n### GRAVY Interpretation\n\n- **GRAVY \u003C -0.5**: Very hydrophilic (highly soluble)\n- **GRAVY -0.5 to 0**: Hydrophilic (soluble)\n- **GRAVY 0 to +0.5**: Hydrophobic (may have solubility issues)\n- **GRAVY > +0.5**: Very hydrophobic (likely membrane-associated or poorly soluble)\n\n### Extinction Coefficient Usage\n\nCalculate peptide concentration:\n```\nConcentration (M) = Absorbance at 280nm \u002F (Extinction Coefficient × Path Length)\n```\n\nWhere path length is typically 1 cm for standard cuvettes.\n\n**Note**: Extinction coefficient is primarily determined by Trp (5500), Tyr (1490), and Cys-Cys (125) residues.\n\n### Additional Peptide Tools Available\n\n- `ConvertingPeptide2SMILES`: Convert peptide sequence to SMILES notation\n- `ProteinIsoelectricPointCalculator`: Calculate pI for longer sequences\n- `ComputeAffinity`: Predict peptide-protein binding affinity\n- `OverlapPeptideLibraryDesign`: Design peptide libraries\n- `AlanineScanningLibraryDesign`: Design mutagenesis libraries\n- `TruncationLibraryDesign`: Design truncation variants\n","# Peptide Properties Calculation\n\n## Usage\n\n### 1. MCP Server Definition\n\nUse the same `BiologyToolsClient` class as defined in the protein-properties-calculation skill.\n\n### 2. Peptide Properties Calculation Workflow\n\nThis workflow calculates comprehensive physicochemical properties of peptide sequences for peptide drug design, synthesis planning, and characterization.\n\n**Workflow Steps:**\n\n1. **Calculate Peptide Properties** - Compute MW, pI, extinction coefficient, GRAVY, and chemical formula\n2. **Analyze Multiple Peptides** - Compare properties across different sequences\n\n**Implementation:**\n\n```python\n## Initialize client\nHEADERS = {\"SCP-HUB-API-KEY\": \"\u003Cyour-api-key>\"}\n\nclient = BiologyToolsClient(\n    \"https:\u002F\u002Fscp.intern-ai.org.cn\u002Fapi\u002Fv1\u002Fmcp\u002F29\u002FSciToolAgent-Bio\",\n    HEADERS\n)\n\nif not await client.connect():\n    print(\"connection failed\")\n    exit()\n\nprint(\"=== Peptide Properties Calculation ===\\n\")\n\n## Input: Peptide sequences to analyze\npeptides = [\n    (\"All 20 amino acids\", \"ACDEFGHIKLMNPQRSTVWY\"),\n    (\"Glycine repeat\", \"GGGGG\"),\n    (\"Arginine repeat (positively charged)\", \"RRRRR\"),\n]\n\n## Calculate properties for each peptide\nfor name, peptide in peptides:\n    print(f\"--- {name}: {peptide} ---\")\n\n    # Calculate peptide properties\n    result = await client.client.call_tool(\n        \"CalculatorPeptideProperty\",\n        arguments={\n            \"sq\": peptide,\n            \"aaCode\": \"0\",          # Use single-letter code\n            \"nTerm\": \"\",            # N-terminal modification (if any)\n            \"cTerm\": \"\",            # C-terminal modification (if any)\n            \"disulphideBonds\": \"\"   # Disulfide bonds (if any)\n        }\n    )\n    result_data = client.parse_result(result)\n    print(f\"{result_data}\\n\")\n\n## Additional analysis: Peptide weight calculation\nprint(\"=== Peptide Weight Calculation (Alternative Method) ===\\n\")\ntest_peptide = \"ACDEFGHIKLMNPQRSTVWY\"\n\nresult = await client.client.call_tool(\n    \"PeptideWeightCalculator\",\n    arguments={\"sequence\": test_peptide}\n)\nresult_data = client.parse_result(result)\nprint(f\"Peptide: {test_peptide}\")\nprint(f\"{result_data}\\n\")\n\n## Additional analysis: Peptide formula calculation\nprint(\"=== Peptide Chemical Formula ===\\n\")\n\nresult = await client.client.call_tool(\n    \"PeptideFormulaCalculator\",\n    arguments={\"sequence\": test_peptide}\n)\nresult_data = client.parse_result(result)\nprint(f\"Peptide: {test_peptide}\")\nprint(f\"{result_data}\\n\")\n\nawait client.disconnect()\n```\n\n### Tool Descriptions\n\n**SciToolAgent-Bio Server:**\n- `CalculatorPeptideProperty`: Calculate comprehensive peptide properties\n  - Args:\n    - `sq` (str): Peptide sequence (single or three-letter code)\n    - `aaCode` (str): \"0\" for single-letter, \"1\" for three-letter code\n    - `nTerm` (str): N-terminal modification (e.g., \"Acetyl\", \"\")\n    - `cTerm` (str): C-terminal modification (e.g., \"Amide\", \"\")\n    - `disulphideBonds` (str): Disulfide bonds specification\n  - Returns: MW, extinction coefficient, pI, GRAVY, chemical formula, sequence length\n\n- `PeptideWeightCalculator`: Calculate peptide molecular weight\n  - Args: `sequence` (str) - Peptide sequence\n  - Returns: Molecular weight in Daltons\n\n- `PeptideFormulaCalculator`: Calculate peptide chemical formula\n  - Args: `sequence` (str) - Peptide sequence\n  - Returns: Molecular formula (e.g., C₁₀₇H₁₅₉N₂₉O₃₀S₂)\n\n### Input\u002FOutput\n\n**Input:**\n- `sq`: Peptide sequence in single-letter (ACDEFG...) or three-letter (Ala-Cys-Asp...) code\n- `aaCode`: \"0\" for single-letter code, \"1\" for three-letter code\n- `nTerm`: Optional N-terminal modification\n- `cTerm`: Optional C-terminal modification\n- `disulphideBonds`: Optional disulfide bond specification\n\n**Output:**\n- **Average Molecular Weight**: Mass in g\u002Fmol or Daltons\n- **Extinction Coefficient**: For peptide quantification at 280nm (M⁻¹cm⁻¹)\n- **Theoretical Isoelectric Point (pI)**: pH at which peptide has no net charge\n- **GRAVY (Grand Average of Hydropathy)**: Hydrophobicity index\n- **Chemical Formula**: Elemental composition (C, H, N, O, S)\n- **Sequence Length**: Number of amino acid residues\n- **Three-letter Representation**: Full peptide notation\n\n### Use Cases\n\n- Design peptide drugs and therapeutics\n- Plan peptide synthesis strategies\n- Calculate peptide concentrations spectrophotometrically\n- Predict peptide solubility and stability\n- Optimize peptide purification conditions\n- Design peptide-based biosensors\n- Analyze peptide fragments from mass spectrometry\n\n### Terminal Modifications\n\nCommon N-terminal modifications:\n- **Acetyl**: Blocks N-terminus, increases stability\n- **Formyl**: Common in bacterial proteins\n- **None**: Free amine group (default)\n\nCommon C-terminal modifications:\n- **Amide**: Blocks C-terminus, increases stability\n- **None**: Free carboxyl group (default)\n\nExample with modifications:\n```python\nresult = await client.client.call_tool(\n    \"CalculatorPeptideProperty\",\n    arguments={\n        \"sq\": \"ACDEFG\",\n        \"aaCode\": \"0\",\n        \"nTerm\": \"Acetyl\",\n        \"cTerm\": \"Amide\",\n        \"disulphideBonds\": \"\"\n    }\n)\n```\n\n### GRAVY Interpretation\n\n- **GRAVY \u003C -0.5**: Very hydrophilic (highly soluble)\n- **GRAVY -0.5 to 0**: Hydrophilic (soluble)\n- **GRAVY 0 to +0.5**: Hydrophobic (may have solubility issues)\n- **GRAVY > +0.5**: Very hydrophobic (likely membrane-associated or poorly soluble)\n\n### Extinction Coefficient Usage\n\nCalculate peptide concentration:\n```\nConcentration (M) = Absorbance at 280nm \u002F (Extinction Coefficient × Path Length)\n```\n\nWhere path length is typically 1 cm for standard cuvettes.\n\n**Note**: Extinction coefficient is primarily determined by Trp (5500), Tyr (1490), and Cys-Cys (125) residues.\n\n### Additional Peptide Tools Available\n\n- `ConvertingPeptide2SMILES`: Convert peptide sequence to SMILES notation\n- 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For formulating testable hypotheses from data use hypothesis-generation.","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fthinking\u002Fscientific-brainstorming\u002FSKILL.md",[],[161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,148],"brainstorming","scientific brainstorming","research ideation","stage","connections","generation","exploration","do","planning","creative","ideation","research","sessions","data","hypothesis","open",{"skillNo":178,"name":179,"nameZh":6,"description":180,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":181,"categories":182,"keywords":187,"publishedAt":31},"01M6DMPV4AMCCTWARGPSFHDWJB","scientific-literature-search","Search scientific literature and research papers using FlowSearch to find relevant academic articles and publications.","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fsearch\u002Fscientific-literature-search\u002FSKILL.md",[183,186],{"categoryNo":184,"categoryName":185,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000021","资料检索与研究",{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[188,189,172,190,191,192],"search","scientific literature search","find","Academic","搜索",{"skillNo":194,"name":195,"nameZh":6,"description":196,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":197,"categories":198,"keywords":205,"publishedAt":31},"01M6DMPQJP8HVFV54V05D6K9HA","pubmed-article-search","Search PubMed database for scientific articles and publications to retrieve biomedical literature.","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fsearch\u002Fpubmed-article-search\u002FSKILL.md",[199,202],{"categoryNo":200,"categoryName":201,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000018","写作与文案",{"categoryNo":203,"categoryName":204,"taxonomyType":131,"taxonomyTypeDesc":132},"01JBSEEDCAT000000000000036","内容创作者",[206,207,188,192,208,209,210],"pubmed article search","article","database","pubmed database","biomedical",{"skillNo":212,"name":213,"nameZh":6,"description":214,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":215,"categories":216,"keywords":218,"publishedAt":31},"01M6DMPK4H3JQ185M97BRB9KQJ","biomedical-web-search","Search biomedical literature and web content using Tavily search engine for research and clinical information.","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fsearch\u002Fbiomedical-web-search\u002FSKILL.md",[217],{"categoryNo":184,"categoryName":185,"taxonomyType":21,"taxonomyTypeDesc":22},[219,210,220,188,221,222,172,223,224,192,225],"biomedical web search","web search","web","tavily","content","engine","clinical",{"skillNo":227,"name":228,"nameZh":6,"description":229,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":230,"categories":231,"keywords":233,"publishedAt":31},"01M6DMNNJH9V1S5PQHZRX0N934","uniprot-protein-retrieval","Retrieve protein sequences and functional information from UniProt database by protein name, enabling protein analysis and bioinformatics workflows.","https:\u002F\u002Fgithub.com\u002FInternScience\u002FDrClaw\u002Fblob\u002Fmain\u002Fdrclaw\u002Flocal_skill_hub\u002Fscience\u002Fprotein\u002Funiprot-protein-retrieval\u002FSKILL.md",[232],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[234,208,141,235,236,237,238],"uniprot protein retrieval","uniprot database","bioinformatics","name","workflows"]