Protein Structure Analysis calculates various physicochemical properties and structural features of protein sequences. This includes:
- **Amino acid composition**: Percentage of each amino acid - **Molecular weight**: Calculated from sequence - **Isoelectric point (pI)**: pH at which protein has no net charge - **Hydropathy**: Hydrophobicity analysis - **Structural predictions**: Secondary structure predictions
Applications
- Protein characterization - Functional prediction - Experimental design - Comparative analysis
Required
- Protein sequence in single-letter amino acid code - FASTA format (with or without header) - Raw amino acid sequence
Valid amino acids
A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y
Example input
``` MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVGDGTQDNLSGAEKAVQVKVKALPDAQFEVVHSLAKWKRQTLGQHDFSAGEGLYTHMKALRPDEDRLSPLHSVYVDQWDWERVMGDGERQFSTLKSTVEAIWAGIKATEAAVSEEFGLAPFLPDQIHFVHSQELLSRYPDLDAKGRERAIAKDLGAVFLVGIGGKLSDGHRHDVRAPDYDDWSTPSELGHAGLNGDILVWNPVLEDAFELSSMGIRVDADTLKHQLALTGDEDRLELEWHQALLRGEMPQTIGGGIGQSRLTMLLLQLPHIGQVQAGVWPAAVRESVPSLL
Protein Properties
- **Molecular Weight**: Calculated from amino acid composition (in Daltons) - **Isoelectric Point (pI)**: pH value where net charge is zero - **Amino Acid Composition**: Count and percentage of each amino acid type
Structural Features
- **Hydrophobicity**: Analysis of hydrophobic vs. hydrophilic regions - **Charge distribution**: Distribution of charged amino acids - **Aromatic content**: Percentage of aromatic amino acids
Predictions
- Secondary structure predictions (if available) - Transmembrane regions (if applicable) - Signal peptides (if applicable)
**1. Protein Characterization** - Characterize newly identified proteins - Compare protein properties across homologs - Study protein families
**2. Experimental Design** - Predict protein solubility - Design purification strategies - Estimate protein behavior under different conditions
**3. Functional Prediction** - Predict protein function from properties - Identify potential binding sites - Study structure-function relationships
1. **Complete sequences**: Use complete protein sequences for accurate calculations 2. **Signal peptides**: Consider removing signal peptides for mature protein analysis 3. **Post-translational modifications**: Note that some properties may change with PTMs 4. **Comparative analysis**: Compare properties across related proteins 5. **Experimental validation**: Validate predictions with experimental data when possible