[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"skill:01M6DMKCGEDCJ8EZH3ECM471DW":3,"skill-same:01M6DMKCGEDCJ8EZH3ECM471DW":110},{"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":29,"linkOnly":30,"markdownContent":31,"markdownBody":32,"frontMatter":33,"refName":40,"commitSha":41,"skillDirectory":42,"forksCount":43,"repositoryHtmlUrl":44,"repositoryHomepageUrl":6,"ownerHtmlUrl":45,"ownerBlogUrl":6,"ownerDescription":46,"updatedAt":47,"install":48,"resources":61},"01M6DMKCGEDCJ8EZH3ECM471DW","protein-properties-calculation",null,"Calculate comprehensive protein sequence properties including isoelectric point, molecular weight, hydrophobicity, and physicochemical parameters.","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\u002Fprotein-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],"properties","protein properties calculation","计算","calculate","molecular","2026-11-10 10:12:30",false,"---\nname: protein-properties-calculation\ndescription: Calculate comprehensive protein sequence properties including isoelectric\n  point, molecular weight, hydrophobicity, and physicochemical parameters.\nlicense: MIT license\nmetadata:\n  skill-author: PJLab\ni18n:\n  zh:\n    description: 计算蛋白质序列理化性质。\n---\n\n# Protein Properties Calculation\n\n## Usage\n\n### 1. MCP Server Definition\n\n```python\nimport asyncio\nimport json\nfrom fastmcp import Client\nfrom fastmcp.client.transports import StreamableHttpTransport\n\nclass BiologyToolsClient:\n    \"\"\"Biology Tools MCP Client using FastMCP\"\"\"\n\n    def __init__(self, server_url: str, headers: dict = None):\n        self.server_url = server_url\n        self.headers = headers or {}\n        self.client = None\n\n    async def connect(self):\n        \"\"\"Establish connection and initialize session\"\"\"\n        print(f\"Connecting to: {self.server_url}\")\n        try:\n            transport = StreamableHttpTransport(\n                url=self.server_url,\n                headers=self.headers\n            )\n\n            self.client = Client(transport)\n            await self.client.__aenter__()\n\n            print(f\"✓ connect success\")\n            return True\n\n        except Exception as e:\n            print(f\"✗ connect failure: {e}\")\n            import traceback\n            traceback.print_exc()\n            return False\n\n    async def disconnect(self):\n        \"\"\"Disconnect from server\"\"\"\n        try:\n            if self.client:\n                await self.client.__aexit__(None, None, None)\n            print(\"✓ already disconnect\")\n        except Exception as e:\n            print(f\"✗ disconnect error: {e}\")\n\n    def parse_result(self, result):\n        \"\"\"Parse MCP tool call result\"\"\"\n        try:\n            if hasattr(result, 'content') and result.content:\n                content = result.content[0]\n                if hasattr(content, 'text'):\n                    try:\n                        return json.loads(content.text)\n                    except:\n                        return content.text\n            return str(result)\n        except Exception as e:\n            return {\"error\": f\"parse error: {e}\", \"raw\": str(result)}\n```\n\n### 2. Protein Properties Calculation Workflow\n\nThis workflow calculates comprehensive physicochemical properties of protein sequences including molecular weight, isoelectric point, hydrophobicity, and other parameters useful for protein characterization.\n\n**Workflow Steps:**\n\n1. **Calculate Isoelectric Point and Molecular Weight** - Compute pI and MW\n2. **Calculate Protein Parameters** - Compute amino acid composition, instability index, etc.\n3. **Calculate Hydrophobicity** - Predict hydrophobic\u002Fhydrophilic regions\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\n## Input: Protein sequence to analyze\nprotein_sequence = \"MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL\"\n\nprint(\"=== Protein Properties Calculation ===\\n\")\n\n## Step 1: Calculate isoelectric point and molecular weight\nprint(\"Step 1: Isoelectric Point and Molecular Weight\")\nresult = await client.client.call_tool(\n    \"ComputePiMw\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 2: Calculate comprehensive protein parameters\nprint(\"Step 2: Protein Sequence Parameters\")\nresult = await client.client.call_tool(\n    \"ComputeProtPara\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 3: Calculate hydrophobicity scale\nprint(\"Step 3: Hydrophobicity Profile\")\nresult = await client.client.call_tool(\n    \"ComputeProtScale\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 4: Calculate extinction coefficient\nprint(\"Step 4: Extinction Coefficient\")\nresult = await client.client.call_tool(\n    \"ComputeExtinctionCoefficient\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\nawait client.disconnect()\n```\n\n### Tool Descriptions\n\n**SciToolAgent-Bio Server:**\n- `ComputePiMw`: Calculate protein isoelectric point and molecular weight\n  - Args: `protein` (str) - Protein sequence\n  - Returns: pI value and molecular weight in Daltons\n\n- `ComputeProtPara`: Calculate comprehensive protein parameters\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Amino acid composition, instability index, aliphatic index, GRAVY, etc.\n\n- `ComputeProtScale`: Calculate hydrophobicity scale\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Hydrophobicity values along the sequence\n\n- `ComputeExtinctionCoefficient`: Calculate extinction coefficient at 280nm\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Extinction coefficient for protein quantification\n\n### Input\u002FOutput\n\n**Input:**\n- `protein`: Protein sequence in single-letter amino acid code\n\n**Output:**\n- **pI (Isoelectric Point)**: pH at which protein has no net charge\n- **Molecular Weight**: Mass in Daltons (Da)\n- **Amino Acid Composition**: Percentage of each amino acid\n- **Instability Index**: Protein stability estimate (>40 = unstable)\n- **Aliphatic Index**: Thermal stability indicator\n- **GRAVY (Grand Average of Hydropathy)**: Overall hydrophobicity (-2 to +2)\n- **Extinction Coefficient**: For protein concentration determination (M⁻¹cm⁻¹)\n\n### Use Cases\n\n- Predict protein behavior in different pH conditions\n- Estimate protein molecular weight from sequence\n- Assess protein stability and solubility\n- Determine protein concentration spectrophotometrically\n- Plan protein purification strategies\n- Predict protein localization based on hydrophobicity\n- Design expression and purification protocols\n\n### Parameter Interpretation\n\n- **pI \u003C 7**: Acidic protein (negatively charged at physiological pH)\n- **pI > 7**: Basic protein (positively charged at physiological pH)\n- **Instability Index \u003C 40**: Stable protein\n- **Instability Index > 40**: Unstable protein (may degrade quickly)\n- **GRAVY \u003C 0**: Hydrophilic (soluble in water)\n- **GRAVY > 0**: Hydrophobic (may be membrane protein or have stability issues)\n\n### Additional Tools Available\n\nThe SciToolAgent-Bio server provides 50+ additional tools including:\n- Codon optimization (`ProteinCodonOptimization`)\n- Peptide weight calculation (`PeptideWeightCalculator`)\n- Protein solubility prediction (`ProteinSolubilityPredictor`)\n- Disordered region prediction (`InherentDisorderedRegionsPredictor`)\n- Nuclear localization signal prediction (`ProteinNuclearLocalizationSequencePrediction`)\n","# Protein Properties Calculation\n\n## Usage\n\n### 1. MCP Server Definition\n\n```python\nimport asyncio\nimport json\nfrom fastmcp import Client\nfrom fastmcp.client.transports import StreamableHttpTransport\n\nclass BiologyToolsClient:\n    \"\"\"Biology Tools MCP Client using FastMCP\"\"\"\n\n    def __init__(self, server_url: str, headers: dict = None):\n        self.server_url = server_url\n        self.headers = headers or {}\n        self.client = None\n\n    async def connect(self):\n        \"\"\"Establish connection and initialize session\"\"\"\n        print(f\"Connecting to: {self.server_url}\")\n        try:\n            transport = StreamableHttpTransport(\n                url=self.server_url,\n                headers=self.headers\n            )\n\n            self.client = Client(transport)\n            await self.client.__aenter__()\n\n            print(f\"✓ connect success\")\n            return True\n\n        except Exception as e:\n            print(f\"✗ connect failure: {e}\")\n            import traceback\n            traceback.print_exc()\n            return False\n\n    async def disconnect(self):\n        \"\"\"Disconnect from server\"\"\"\n        try:\n            if self.client:\n                await self.client.__aexit__(None, None, None)\n            print(\"✓ already disconnect\")\n        except Exception as e:\n            print(f\"✗ disconnect error: {e}\")\n\n    def parse_result(self, result):\n        \"\"\"Parse MCP tool call result\"\"\"\n        try:\n            if hasattr(result, 'content') and result.content:\n                content = result.content[0]\n                if hasattr(content, 'text'):\n                    try:\n                        return json.loads(content.text)\n                    except:\n                        return content.text\n            return str(result)\n        except Exception as e:\n            return {\"error\": f\"parse error: {e}\", \"raw\": str(result)}\n```\n\n### 2. Protein Properties Calculation Workflow\n\nThis workflow calculates comprehensive physicochemical properties of protein sequences including molecular weight, isoelectric point, hydrophobicity, and other parameters useful for protein characterization.\n\n**Workflow Steps:**\n\n1. **Calculate Isoelectric Point and Molecular Weight** - Compute pI and MW\n2. **Calculate Protein Parameters** - Compute amino acid composition, instability index, etc.\n3. **Calculate Hydrophobicity** - Predict hydrophobic\u002Fhydrophilic regions\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\n## Input: Protein sequence to analyze\nprotein_sequence = \"MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL\"\n\nprint(\"=== Protein Properties Calculation ===\\n\")\n\n## Step 1: Calculate isoelectric point and molecular weight\nprint(\"Step 1: Isoelectric Point and Molecular Weight\")\nresult = await client.client.call_tool(\n    \"ComputePiMw\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 2: Calculate comprehensive protein parameters\nprint(\"Step 2: Protein Sequence Parameters\")\nresult = await client.client.call_tool(\n    \"ComputeProtPara\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 3: Calculate hydrophobicity scale\nprint(\"Step 3: Hydrophobicity Profile\")\nresult = await client.client.call_tool(\n    \"ComputeProtScale\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\n## Step 4: Calculate extinction coefficient\nprint(\"Step 4: Extinction Coefficient\")\nresult = await client.client.call_tool(\n    \"ComputeExtinctionCoefficient\",\n    arguments={\"protein\": protein_sequence}\n)\nresult_data = client.parse_result(result)\nprint(f\"{result_data}\\n\")\n\nawait client.disconnect()\n```\n\n### Tool Descriptions\n\n**SciToolAgent-Bio Server:**\n- `ComputePiMw`: Calculate protein isoelectric point and molecular weight\n  - Args: `protein` (str) - Protein sequence\n  - Returns: pI value and molecular weight in Daltons\n\n- `ComputeProtPara`: Calculate comprehensive protein parameters\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Amino acid composition, instability index, aliphatic index, GRAVY, etc.\n\n- `ComputeProtScale`: Calculate hydrophobicity scale\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Hydrophobicity values along the sequence\n\n- `ComputeExtinctionCoefficient`: Calculate extinction coefficient at 280nm\n  - Args: `protein` (str) - Protein sequence\n  - Returns: Extinction coefficient for protein quantification\n\n### Input\u002FOutput\n\n**Input:**\n- `protein`: Protein sequence in single-letter amino acid code\n\n**Output:**\n- **pI (Isoelectric Point)**: pH at which protein has no net charge\n- **Molecular Weight**: Mass in Daltons (Da)\n- **Amino Acid Composition**: Percentage of each amino acid\n- **Instability Index**: Protein stability estimate (>40 = unstable)\n- **Aliphatic Index**: Thermal stability indicator\n- **GRAVY (Grand Average of Hydropathy)**: Overall hydrophobicity (-2 to +2)\n- **Extinction Coefficient**: For protein concentration determination (M⁻¹cm⁻¹)\n\n### Use Cases\n\n- Predict protein behavior in different pH conditions\n- Estimate protein molecular weight from sequence\n- Assess protein stability and solubility\n- Determine protein concentration spectrophotometrically\n- Plan protein purification strategies\n- Predict protein localization based on hydrophobicity\n- Design expression and purification protocols\n\n### Parameter Interpretation\n\n- **pI \u003C 7**: Acidic protein (negatively charged at physiological pH)\n- **pI > 7**: Basic protein (positively charged at physiological pH)\n- **Instability Index \u003C 40**: Stable protein\n- **Instability Index > 40**: Unstable protein (may degrade quickly)\n- **GRAVY \u003C 0**: Hydrophilic (soluble in water)\n- **GRAVY > 0**: Hydrophobic (may be membrane protein or have stability issues)\n\n### Additional Tools Available\n\nThe SciToolAgent-Bio server provides 50+ additional tools including:\n- Codon optimization (`ProteinCodonOptimization`)\n- Peptide weight calculation (`PeptideWeightCalculator`)\n- Protein 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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",[],[153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,140],"brainstorming","scientific brainstorming","research ideation","stage","connections","generation","exploration","do","planning","creative","ideation","research","sessions","data","hypothesis","open",{"skillNo":170,"name":171,"nameZh":6,"description":172,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":173,"categories":174,"keywords":179,"publishedAt":29},"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",[175,178],{"categoryNo":176,"categoryName":177,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000021","资料检索与研究",{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[180,181,164,182,183,184],"search","scientific literature search","find","Academic","搜索",{"skillNo":186,"name":187,"nameZh":6,"description":188,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":189,"categories":190,"keywords":197,"publishedAt":29},"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",[191,194],{"categoryNo":192,"categoryName":193,"taxonomyType":21,"taxonomyTypeDesc":22},"01JBSEEDCAT000000000000018","写作与文案",{"categoryNo":195,"categoryName":196,"taxonomyType":123,"taxonomyTypeDesc":124},"01JBSEEDCAT000000000000036","内容创作者",[198,199,180,184,200,201,202],"pubmed article search","article","database","pubmed database","biomedical",{"skillNo":204,"name":205,"nameZh":6,"description":206,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":207,"categories":208,"keywords":210,"publishedAt":29},"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",[209],{"categoryNo":176,"categoryName":177,"taxonomyType":21,"taxonomyTypeDesc":22},[211,202,212,180,213,214,164,215,216,184,217],"biomedical web search","web search","web","tavily","content","engine","clinical",{"skillNo":219,"name":220,"nameZh":6,"description":221,"descriptionZh":6,"repositoryFullName":8,"ownerLogin":9,"ownerAvatarUrl":10,"ownerAccountNo":11,"ownerDisplayName":12,"repositoryNo":13,"starsCount":14,"licenseSpdxId":15,"licenseFileUrl":6,"sourceHtmlUrl":222,"categories":223,"keywords":225,"publishedAt":29},"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",[224],{"categoryNo":19,"categoryName":20,"taxonomyType":21,"taxonomyTypeDesc":22},[226,200,133,227,228,229,230],"uniprot protein retrieval","uniprot database","bioinformatics","name","workflows"]