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version: "1.0.1" name: protein-properties-calculation 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 asyncioimport jsonfrom fastmcp import Clientfrom fastmcp.client.transports import StreamableHttpTransportclass BiologyToolsClient:"""Biology Tools MCP Client using FastMCP"""def __init__(self, server_url: str, headers: dict = None):self.server_url = server_urlself.headers = headers or {}self.client = Noneasync 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 Trueexcept Exception as e:print(f"✗ connect failure: {e}")import tracebacktraceback.print_exc()return Falseasync 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.textreturn 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:
- Calculate Isoelectric Point and Molecular Weight - Compute pI and MW
- Calculate Protein Parameters - Compute amino acid composition, instability index, etc.
- Calculate Hydrophobicity - Predict hydrophobic/hydrophilic regions
Implementation:
python
## Initialize clientHEADERS = {"SCP-HUB-API-KEY": "<your-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 analyzeprotein_sequence = "MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL"print("=== Protein Properties Calculation ===\n")## Step 1: Calculate isoelectric point and molecular weightprint("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 parametersprint("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 scaleprint("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 coefficientprint("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)