--- name: peptide-properties-calculation description: Calculate peptide sequence properties including molecular weight, isoelectric point, extinction coefficient, and chemical formula. license: MIT license metadata: skill-author: PJLab --- # Peptide Properties Calculation ## Usage ### 1. MCP Server Definition Use the same `BiologyToolsClient` class as defined in the protein-properties-calculation skill. ### 2. Peptide Properties Calculation Workflow This workflow calculates comprehensive physicochemical properties of peptide sequences for peptide drug design, synthesis planning, and characterization. **Workflow Steps:** 1. **Calculate Peptide Properties** - Compute MW, pI, extinction coefficient, GRAVY, and chemical formula 2. **Analyze Multiple Peptides** - Compare properties across different sequences **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() 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() ``` ### Tool Descriptions **SciToolAgent-Bio Server:** - `CalculatorPeptideProperty`: Calculate comprehensive peptide properties - Args: - `sq` (str): Peptide sequence (single or three-letter code) - `aaCode` (str): "0" for single-letter, "1" for three-letter code - `nTerm` (str): N-terminal modification (e.g., "Acetyl", "") - `cTerm` (str): C-terminal modification (e.g., "Amide", "") - `disulphideBonds` (str): Disulfide bonds specification - Returns: MW, extinction coefficient, pI, GRAVY, chemical formula, sequence length - `PeptideWeightCalculator`: Calculate peptide molecular weight - Args: `sequence` (str) - Peptide sequence - Returns: Molecular weight in Daltons - `PeptideFormulaCalculator`: Calculate peptide chemical formula - Args: `sequence` (str) - Peptide sequence - Returns: Molecular formula (e.g., C₁₀₇H₁₅₉N₂₉O₃₀S₂) ### Input/Output **Input:** - `sq`: Peptide sequence in single-letter (ACDEFG...) or three-letter (Ala-Cys-Asp...) code - `aaCode`: "0" for single-letter code, "1" for three-letter code - `nTerm`: Optional N-terminal modification - `cTerm`: Optional C-terminal modification - `disulphideBonds`: Optional disulfide bond specification **Output:** - **Average Molecular Weight**: Mass in g/mol or Daltons - **Extinction Coefficient**: For peptide quantification at 280nm (M⁻¹cm⁻¹) - **Theoretical Isoelectric Point (pI)**: pH at which peptide has no net charge - **GRAVY (Grand Average of Hydropathy)**: Hydrophobicity index - **Chemical Formula**: Elemental composition (C, H, N, O, S) - **Sequence Length**: Number of amino acid residues - **Three-letter Representation**: Full peptide notation ### Use Cases - Design peptide drugs and therapeutics - Plan peptide synthesis strategies - Calculate peptide concentrations spectrophotometrically - Predict peptide solubility and stability - Optimize peptide purification conditions - Design peptide-based biosensors - Analyze peptide fragments from mass spectrometry ### Terminal Modifications Common N-terminal modifications: - **Acetyl**: Blocks N-terminus, increases stability - **Formyl**: Common in bacterial proteins - **None**: Free amine group (default) Common C-terminal modifications: - **Amide**: Blocks C-terminus, increases stability - **None**: Free carboxyl group (default) Example with modifications: ```python result = await client.client.call_tool( "CalculatorPeptideProperty", arguments={ "sq": "ACDEFG", "aaCode": "0", "nTerm": "Acetyl", "cTerm": "Amide", "disulphideBonds": "" } ) ``` ### GRAVY Interpretation - **GRAVY < -0.5**: Very hydrophilic (highly soluble) - **GRAVY -0.5 to 0**: Hydrophilic (soluble) - **GRAVY 0 to +0.5**: Hydrophobic (may have solubility issues) - **GRAVY > +0.5**: Very hydrophobic (likely membrane-associated or poorly soluble) ### Extinction Coefficient Usage 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. ### Additional Peptide Tools Available - `ConvertingPeptide2SMILES`: Convert peptide sequence to SMILES notation - `ProteinIsoelectricPointCalculator`: Calculate pI for longer sequences - `ComputeAffinity`: Predict peptide-protein binding affinity - `OverlapPeptideLibraryDesign`: Design peptide libraries - `AlanineScanningLibraryDesign`: Design mutagenesis libraries - `TruncationLibraryDesign`: Design truncation variants --- Source attribution: InternScience Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/peptide-properties-calculation/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Dave AI. ## 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. # Dave AI resource metadata Creator / publisher: InternScience Original project: https://github.com/InternScience/scp/blob/cea5398564032aea65a78e246d06c30ae945e03f/skills/peptide-properties-calculation/SKILL.md Attribution basis: Source repository record Fields of work: Data & Analytics, Education & Research, Healthcare & Life Sciences Roles: Business Intelligence Analyst, Clinical Research, Researcher Specialties: API Tools: Biologytoolsclient Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: ef5cdac02f3f43bbd40cf48ad9819c557c318084a315aa719be56f66e9923595