Protein Properties Calculation

Protein Properties Calculation

Usage

1. MCP Server Definition

import asyncio
import json
from contextlib import AsyncExitStack
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._stack = AsyncExitStack()
            await self._stack.__aenter__()
            self.client = Client(transport)
            await self._stack.enter_async_context(self.client)

            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 hasattr(self, '_stack'):
                await self._stack.aclose()
            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:

## Initialize client
HEADERS = {"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 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)