Protein analysis tools
Protein Analysis Tools
ProteinIQ offers a comprehensive suite of protein analysis tools that calculate various physicochemical properties of protein sequences. All calculations are performed locally in your browser for maximum privacy and speed.
Available Analysis Tools
Molecular Weight Calculator
Calculate the molecular weight of protein sequences with high precision.
Features:
- Accurate molecular weight calculation in Daltons
- Support for standard 20 amino acids
- Handles modified amino acids
- Batch processing capabilities
Usage:
- Input your protein sequence in FASTA format
- Click "Calculate" to get instant results
- Results include total molecular weight and amino acid composition
Isoelectric Point (pI) Calculator
Determine the pH at which a protein carries no net electrical charge.
Key Information:
- Uses Henderson-Hasselbalch equation
- Considers all ionizable groups
- Accurate for pH range 0-14
- Essential for protein purification planning
Applications:
- Protein purification strategy
- Electrophoresis planning
- Buffer selection
- Protein stability assessment
Instability Index
Assess the stability of proteins based on amino acid composition.
Interpretation:
- Index < 40: Stable protein
- Index > 40: Unstable protein
- Based on statistical analysis of known stable/unstable proteins
Use Cases:
- Protein engineering projects
- Expression system selection
- Storage condition optimization
GRAVY Score (Grand Average of Hydropathy)
Calculate the overall hydrophobicity of protein sequences.
Score Interpretation:
- Positive values: Hydrophobic proteins
- Negative values: Hydrophilic proteins
- Range typically -2.0 to +2.0
Applications:
- Membrane protein identification
- Protein localization prediction
- Solubility assessment
Aliphatic Index
Measure the relative volume occupied by aliphatic side chains.
Significance:
- Higher values indicate greater thermostability
- Useful for thermophilic protein analysis
- Range: 0-200+ (typical proteins: 70-100)
Research Applications:
- Thermostability engineering
- Industrial enzyme development
- Evolutionary studies
Extinction Coefficient
Calculate molar extinction coefficient for protein concentration determination.
Methods Available:
- Edelhoch method (280 nm)
- Gill and von Hippel method
- Considers Trp, Tyr, and Cys contributions
Laboratory Use:
- Protein concentration measurement
- Spectrophotometric analysis
- Quality control in protein production
Input Formats
All protein analysis tools accept:
FASTA Format
>Protein_Name
MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKEKVNEL
Plain Sequence
MKLLILTCLVAVALARPKHPIKHQGLPQEVLNENLLRFFVAPFPEVFGKEKVNEL
Multiple Sequences
- Upload files with multiple sequences
- Batch analysis capabilities
- Results provided for each sequence
Best Practices
Sequence Quality
- Ensure sequences contain only standard amino acid codes
- Remove any ambiguous characters (X, B, Z)
- Verify sequence accuracy before analysis
Result Interpretation
- Consider experimental conditions
- Compare with known protein properties
- Use multiple parameters for comprehensive analysis
Data Management
- Export results for record keeping
- Include analysis parameters in documentation
- Maintain version control for sequence data
Advanced Features
Batch Processing
- Analyze multiple proteins simultaneously
- Export results in CSV format
- Compare properties across protein sets
Custom Parameters
- Adjust calculation methods where applicable
- Modify pH ranges for pI calculations
- Select specific extinction coefficient methods
Integration with Other Tools
- Combine with structure analysis
- Use with sequence conversion tools
- Export data for external analysis
Troubleshooting
Common Issues
- Invalid amino acid codes: Check for non-standard characters
- Empty results: Verify sequence format and content
- Unexpected values: Confirm sequence accuracy
Getting Help
- Review tool-specific documentation
- Check example sequences
- Contact support for complex issues
References and Methods
Each tool implements established methods from peer-reviewed literature:
- Molecular weight: Standard atomic masses
- pI calculation: Henderson-Hasselbalch equation
- Instability index: Guruprasad et al. (1990)
- GRAVY: Kyte & Doolittle (1982)
- Aliphatic index: Ikai (1980)
- Extinction coefficient: Edelhoch (1967), Gill & von Hippel (1989)