Calculate peptide sequence properties including molecular weight, isoelectric point, extinction coefficient, and chemical formula.
Use the same BiologyToolsClient class as defined in the protein-properties-calculation skill.
This workflow calculates comprehensive physicochemical properties of peptide sequences for peptide drug design, synthesis planning, and characterization.
Workflow Steps:
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()
print("=== Peptide Properties Calculation ===\n")
## Input: Peptide sequences to analyze
peptides = [
("All 20 amino acids", "ACDEFGHIKLMNPQRSTVWY"),
("Glycine repeat", "GGGGG"),
("Arginine repeat (positively charged)", "RRRRR"),
]
## Calculate properties for each peptide
for name, peptide in peptides:
print(f"--- {name}: {peptide} ---")
# Calculate peptide properties
result = await client.client.call_tool(
"CalculatorPeptideProperty",
arguments={
"sq": peptide,
"aaCode": "0", # Use single-letter code
"nTerm": "", # N-terminal modification (if any)
"cTerm": "", # C-terminal modification (if any)
"disulphideBonds": "" # Disulfide bonds (if any)
}
)
result_data = client.parse_result(result)
print(f"{result_data}\n")
## Additional analysis: Peptide weight calculation
print("=== Peptide Weight Calculation (Alternative Method) ===\n")
test_peptide = "ACDEFGHIKLMNPQRSTVWY"
result = await client.client.call_tool(
"PeptideWeightCalculator",
arguments={"sequence": test_peptide}
)
result_data = client.parse_result(result)
print(f"Peptide: {test_peptide}")
print(f"{result_data}\n")
## Additional analysis: Peptide formula calculation
print("=== Peptide Chemical Formula ===\n")
result = await client.client.call_tool(
"PeptideFormulaCalculator",
arguments={"sequence": test_peptide}
)
result_data = client.parse_result(result)
print(f"Peptide: {test_peptide}")
print(f"{result_data}\n")
await client.disconnect()
SciToolAgent-Bio Server:
CalculatorPeptideProperty: Calculate comprehensive peptide properties
sq (str): Peptide sequence (single or three-letter code)aaCode (str): "0" for single-letter, "1" for three-letter codenTerm (str): N-terminal modification (e.g., "Acetyl", "")cTerm (str): C-terminal modification (e.g., "Amide", "")disulphideBonds (str): Disulfide bonds specificationPeptideWeightCalculator: Calculate peptide molecular weight
sequence (str) - Peptide sequencePeptideFormulaCalculator: Calculate peptide chemical formula
sequence (str) - Peptide sequenceInput:
sq: Peptide sequence in single-letter (ACDEFG...) or three-letter (Ala-Cys-Asp...) codeaaCode: "0" for single-letter code, "1" for three-letter codenTerm: Optional N-terminal modificationcTerm: Optional C-terminal modificationdisulphideBonds: Optional disulfide bond specificationOutput:
Common N-terminal modifications:
Common C-terminal modifications:
Example with modifications:
result = await client.client.call_tool(
"CalculatorPeptideProperty",
arguments={
"sq": "ACDEFG",
"aaCode": "0",
"nTerm": "Acetyl",
"cTerm": "Amide",
"disulphideBonds": ""
}
)
Calculate peptide concentration:
Concentration (M) = Absorbance at 280nm / (Extinction Coefficient × Path Length)
Where path length is typically 1 cm for standard cuvettes.
Note: Extinction coefficient is primarily determined by Trp (5500), Tyr (1490), and Cys-Cys (125) residues.
ConvertingPeptide2SMILES: Convert peptide sequence to SMILES notationProteinIsoelectricPointCalculator: Calculate pI for longer sequencesComputeAffinity: Predict peptide-protein binding affinityOverlapPeptideLibraryDesign: Design peptide librariesAlanineScanningLibraryDesign: Design mutagenesis librariesTruncationLibraryDesign: Design truncation variants