--- name: protein-properties-calculation-39e13010673d description: Calculate comprehensive protein sequence properties including isoelectric point, molecular weight, hydrophobicity, and physicochemical parameters. license: MIT license metadata: skill-author: PJLab --- # Protein Properties Calculation ## Usage ### 1. MCP Server Definition ```python import asyncio import json from fastmcp import Client from fastmcp.client.transports import StreamableHttpTransport class BiologyToolsClient: """Biology Tools MCP Client using FastMCP""" def __init__(self, server_url: str, headers: dict = None): self.server_url = server_url self.headers = headers or {} self.client = None async def connect(self): """Establish connection and initialize session""" print(f"Connecting to: {self.server_url}") try: transport = StreamableHttpTransport( url=self.server_url, headers=self.headers ) self.client = Client(transport) await self.client.__aenter__() print(f"✓ connect success") return True except Exception as e: print(f"✗ connect failure: {e}") import traceback traceback.print_exc() return False async def disconnect(self): """Disconnect from server""" try: if self.client: await self.client.__aexit__(None, None, None) print("✓ already disconnect") except Exception as e: print(f"✗ disconnect error: {e}") def parse_result(self, result): """Parse MCP tool call result""" try: if hasattr(result, 'content') and result.content: content = result.content[0] if hasattr(content, 'text'): try: return json.loads(content.text) except: return content.text return str(result) except Exception as e: return {"error": f"parse error: {e}", "raw": str(result)} ``` ### 2. Protein Properties Calculation Workflow This workflow calculates comprehensive physicochemical properties of protein sequences including molecular weight, isoelectric point, hydrophobicity, and other parameters useful for protein characterization. **Workflow Steps:** 1. **Calculate Isoelectric Point and Molecular Weight** - Compute pI and MW 2. **Calculate Protein Parameters** - Compute amino acid composition, instability index, etc. 3. **Calculate Hydrophobicity** - Predict hydrophobic/hydrophilic regions **Implementation:** ```python ## Initialize client HEADERS = {"SCP-HUB-API-KEY": ""} client = BiologyToolsClient( "https://scp.intern-ai.org.cn/api/v1/mcp/29/SciToolAgent-Bio", HEADERS ) if not await client.connect(): print("connection failed") exit() ## Input: Protein sequence to analyze protein_sequence = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL" print("=== Protein Properties Calculation ===\n") ## Step 1: Calculate isoelectric point and molecular weight print("Step 1: Isoelectric Point and Molecular Weight") result = await client.client.call_tool( "ComputePiMw", arguments={"protein": protein_sequence} ) result_data = client.parse_result(result) print(f"{result_data}\n") ## Step 2: Calculate comprehensive protein parameters print("Step 2: Protein Sequence Parameters") result = await client.client.call_tool( "ComputeProtPara", arguments={"protein": protein_sequence} ) result_data = client.parse_result(result) print(f"{result_data}\n") ## Step 3: Calculate hydrophobicity scale print("Step 3: Hydrophobicity Profile") result = await client.client.call_tool( "ComputeProtScale", arguments={"protein": protein_sequence} ) result_data = client.parse_result(result) print(f"{result_data}\n") ## Step 4: Calculate extinction coefficient print("Step 4: Extinction Coefficient") result = await client.client.call_tool( "ComputeExtinctionCoefficient", arguments={"protein": protein_sequence} ) result_data = client.parse_result(result) print(f"{result_data}\n") await client.disconnect() ``` ### Tool Descriptions **SciToolAgent-Bio Server:** - `ComputePiMw`: Calculate protein isoelectric point and molecular weight - Args: `protein` (str) - Protein sequence - Returns: pI value and molecular weight in Daltons - `ComputeProtPara`: Calculate comprehensive protein parameters - Args: `protein` (str) - Protein sequence - Returns: Amino acid composition, instability index, aliphatic index, GRAVY, etc. - `ComputeProtScale`: Calculate hydrophobicity scale - Args: `protein` (str) - Protein sequence - Returns: Hydrophobicity values along the sequence - `ComputeExtinctionCoefficient`: Calculate extinction coefficient at 280nm - Args: `protein` (str) - Protein sequence - Returns: Extinction coefficient for protein quantification ### Input/Output **Input:** - `protein`: Protein sequence in single-letter amino acid code **Output:** - **pI (Isoelectric Point)**: pH at which protein has no net charge - **Molecular Weight**: Mass in Daltons (Da) - **Amino Acid Composition**: Percentage of each amino acid - **Instability Index**: Protein stability estimate (>40 = unstable) - **Aliphatic Index**: Thermal stability indicator - **GRAVY (Grand Average of Hydropathy)**: Overall hydrophobicity (-2 to +2) - **Extinction Coefficient**: For protein concentration determination (M⁻¹cm⁻¹) ### Use Cases - Predict protein behavior in different pH conditions - Estimate protein molecular weight from sequence - Assess protein stability and solubility - Determine protein concentration spectrophotometrically - Plan protein purification strategies - Predict protein localization based on hydrophobicity - Design expression and purification protocols ### Parameter Interpretation - **pI < 7**: Acidic protein (negatively charged at physiological pH) - **pI > 7**: Basic protein (positively charged at physiological pH) - **Instability Index < 40**: Stable protein - **Instability Index > 40**: Unstable protein (may degrade quickly) - **GRAVY < 0**: Hydrophilic (soluble in water) - **GRAVY > 0**: Hydrophobic (may be membrane protein or have stability issues) ### Additional Tools Available The SciToolAgent-Bio server provides 50+ additional tools including: - Codon optimization (`ProteinCodonOptimization`) - Peptide weight calculation (`PeptideWeightCalculator`) - Protein solubility prediction (`ProteinSolubilityPredictor`) - Disordered region prediction (`InherentDisorderedRegionsPredictor`) - Nuclear localization signal prediction (`ProteinNuclearLocalizationSequencePrediction`) --- Source attribution: InternScience Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/protein-properties-calculation/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Mega AI Hub. ## Upstream license notice MIT License Copyright (c) 2024 Anthropic, PBC Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Mega AI Hub resource metadata Creator / publisher: InternScience Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/protein-properties-calculation/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics, Education & Research Roles: Data Scientist, Researcher Specialties: API Tools: Fastmcp Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: a3135513abf2f7caa0266b33980a1ab3676c8c0f2bc868b74a4038ce6e5c0009