Protein Properties Calculator for Sequence Analysis and Feature Extraction

Abstract

Calculate comprehensive protein properties including molecular weight, isoelectric point, amino acid composition, hydropathy index, GRAVY score, instability index, and secondary structure predictions from amino acid sequences.

Cleaned Submission Note

This revision replaces a raw JSON display with readable Markdown. The underlying tool description and skill instructions are preserved.

SKILL

SKILL: Protein Properties Calculator

Metadata

• Name: Protein Properties Calculator
• Version: 1.0.0
• Category: biochemical-analysis
• Tags: protein, biophysics, amino-acid, physicochemical

Description

Calculates physicochemical properties of protein sequences, including molecular weight, isoelectric point, amino acid composition, hydrophobicity, and instability index.

Input

Format

• Type: FASTA format protein sequence
• Encoding: UTF-8
• Validation:
  • Only standard 20 amino acid letters (ACDEFGHIKLMNPQRSTVWY) allowed
  • Sequence must not be empty
  • Optional: header line starting with > is ignored

Example Input

>sp|P69905|HBA_HUMAN Hemoglobin subunit alpha
MKVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH
GSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSH
CLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR

Steps

Step 1: Parse Amino Acid Sequence

1. Remove all whitespace and newline characters
2. Remove header line if present (everything after '>')
3. Convert to uppercase
4. Validate: reject if any non-standard amino acid character found
5. Store cleaned sequence

Step 2: Calculate Molecular Weight (MW)

1. Sum molecular weights of all amino acids
2. Subtract (n-1) * 18.015 for peptide bonds (n = sequence length)
3. Add 18.015 for water molecule at N-terminus
4. Unit: Daltons (Da)
5. Precision: 2 decimal places

Step 3: Calculate Isoelectric Point (pI)

1. Use bisection method to find pH where net charge = 0
2. At each pH estimate:
   - Calculate positive charges (N-terminus + K, R, H)
   - Calculate negative charges (C-terminus + D, E)
   - Net charge = positive - negative
3. Search range: pH 0 to 14
4. Precision: 2 decimal places
5. Use Henderson-Hasselbalch equation for ionizable groups

Step 4: Calculate Amino Acid Composition

1. Count occurrences of each of 20 standard amino acids
2. Calculate percentage for each amino acid
3. Return both count and percentage

Step 5: Calculate Grand Average of Hydropathicity (GRAVY)

1. Use Kyte-Doolittle hydropathy scale
2. GRAVY = sum(amino_acid_hydropathy) / sequence_length
3. Positive = hydrophobic, Negative = hydrophilic

Step 6: Calculate Instability Index (II)

1. Use Guruprasad dipeptide instability weights
2. II = (10^5 / sequence_length) * sum(dipeptide_weights)
3. II < 40 = stable protein
4. II >= 40 = unstable protein

Step 7: Generate Complete Properties Report

1. Compile all calculated properties
2. Generate JSON output with all results

Output

Format

• Type: JSON (JavaScript Object Notation)
• Encoding: UTF-8
• Content-Type: application/json

Schema

{
  "status": "success" | "error",
  "sequence": {
    "raw": "original input",
    "cleaned": "cleaned sequence",
    "length": number
  },
  "properties": {
    "molecular_weight": {
      "value": number,
      "unit": "Da"
    },
    "isoelectric_point": {
      "value": number,
      "description": "pH at which net charge is zero"
    },
    "composition": {
      "A": {"count": number, "percentage": number},
      "C": {"count": number, "percentage": number},
      ...
    },
    "hydropathicity": {
      "gravy": number,
      "description": "Kyte-Doolittle GRAVY score"
    },
    "instability_index": {
      "value": number,
      "classification": "stable" | "unstable"
    }
  },
  "metadata": {
    "calculated_at": "ISO timestamp",
    "calculator_version": "1.0.0"
  }
}

Example Output

{
  "status": "success",
  "sequence": {
    "raw": ">sp|P69905|HBA_HUMAN\nMKVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
    "cleaned": "MKVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR",
    "length": 142
  },
  "properties": {
    "molecular_weight": {"value": 15162.87, "unit": "Da"},
    "isoelectric_point": {"value": 9.14, "description": "pH at which net charge is zero"},
    "composition": {
      "A": {"count": 12, "percentage": 8.45},
      "C": {"count": 0, "percentage": 0.0},
      ...
    },
    "hydropathicity": {"gravy": -0.425, "description": "Kyte-Doolittle GRAVY score"},
    "instability_index": {"value": 38.56, "classification": "stable"}
  },
  "metadata": {
    "calculated_at": "2026-04-29T00:00:00Z",
    "calculator_version": "1.0.0"
  }
}

Tools

Primary Implementation

• Python Standard Library: No external dependencies required
• Method: Direct implementation of ProtParam algorithm

Reference Algorithms

• Guruprasad et al. (1990) - Instability Index
• Kyte & Doolittle (1982) - Hydropathy Scale
• Bjellqvist et al. (1994) - pI calculation

Error Handling

Invalid Sequence

{
  "status": "error",
  "error": {
    "code": "INVALID_SEQUENCE",
    "message": "Sequence contains invalid amino acid character(s): X, Z"
  }
}

Empty Sequence

{
  "status": "error",
  "error": {
    "code": "EMPTY_SEQUENCE",
    "message": "Input sequence is empty"
  }
}

Usage Examples

Direct Function Call

from execute import ProteinPropertiesCalculator
calculator = ProteinPropertiesCalculator()
result = calculator.analyze("MKVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR")
print(result)

Command Line

python execute.py --input test_inputs/protein.fasta --output result.json

Notes

• All calculations assume standard amino acids only
• Post-translational modifications (phosphorylation, glycosylation) are not considered
• Disulfide bonds affect protein stability but are not included in basic II calculation

Integrity Note

This is a formatting cleanup revision. It does not introduce a new scientific claim.