SPICE (Structural Protein Interaction Complex Evaluator) is a comprehensive web application
for analyzing protein-protein interactions and interfaces from PDB structure files. It combines a powerful
Flask-based web interface with a custom python package (spice) to provide researchers
with an accessible platform for complex protein structure analysis.
SPICE eliminates the need for command-line expertise, reducing analysis time from 3-5 minutes to just 10-20 seconds for common analyses through an intuitive web interface.
Select either Single Complex Analysis for analyzing one structure, or Multi-Complex Comparison for comparing multiple variants.
Upload a PDB file from your computer or fetch directly from RCSB database using a PDB ID (e.g., 1A2Y).
Choose which calculations to perform: contacts, interface, distances, geometry, SASA, or VDW energy.
Set your preferred parameters such as distance cutoffs, chain selections, and visualization options.
Click "Run Analysis" and wait for results. Most analyses complete in 10-20 seconds.
View interactive visualizations, examine detailed tables, and download results for your research.
Try the "Load Example Structures" feature to quickly explore SPICE's capabilities with pre-configured protein complexes.
Analyze individual protein-protein complex structures to understand their molecular interactions, interfaces, and biophysical properties. SPICE provides six powerful analysis modules that can be used independently or in combination.
Identifies molecular interactions
Interface residues & BSA
Distance matrices & networks
Backbone & side-chain angles
Surface accessibility
Van der Waals energies
Identifies and characterizes molecular interactions between residues across different protein chains. This analysis helps you understand the binding forces stabilizing protein complexes.
| Contact Type | Detection Criteria | Distance Cutoff |
|---|---|---|
| Hydrogen Bonds | Donor-acceptor distance with angle constraints | ≤ 3.5 Å |
| Salt Bridges | Charged residue pairs (Lys/Arg/His ↔ Asp/Glu) | ≤ 4.0 Å |
| Disulfide Bonds | Cysteine sulfur-sulfur distances | ≤ 2.5 Å |
| Hydrophobic Contacts | Nonpolar residue interactions (Ala, Val, Leu, Ile, Met, Phe, Trp, Pro) | ≤ 5.0 Å |
| π-π Stacking | Aromatic ring interactions (Phe, Tyr, Trp, His) | ≤ 7.0 Å (centroid-centroid) |
Hydrogen Bond Detection: Uses geometric criteria including donor-acceptor distance (≤3.5 Å) and angle requirements (donor-H-acceptor angle ≥120°). Identifies potential donors (N, O with H) and acceptors (O, N, S).
Salt Bridge Detection: Searches for ionic interactions between positively charged residues (Lys, Arg, His) and negatively charged residues (Asp, Glu) within 4.0 Å.
π-π Stacking: Calculates distances between aromatic ring centroids and evaluates ring plane orientations (parallel or perpendicular stacking).
| Parameter | Options | Description |
|---|---|---|
| Group A | Chain selection (multiple) | First group of chains (e.g., antibody heavy and light chains) |
| Group B | Chain selection (multiple) | Second group of chains (e.g., antigen) |
| Contact Types | Checkboxes for each type | Select which interactions to analyze (all selected by default) |
| Color Scheme | By Type / By Count | Visualization coloring: by contact type or by number of contacts per residue |
Contact analysis is ideal for understanding antibody-antigen binding, identifying key interaction residues for mutagenesis studies, and comparing binding modes between different complexes.
Identifies residues at the binding interface between molecular groups and calculates the buried surface area (BSA) upon complex formation.
Interface Residue Detection: A residue is considered part of the interface if any of its atoms is within the specified cutoff distance (default 5.0 Å) of any atom in the partner group.
BSA Calculation: Uses FreeSASA algorithm (Lee & Richards method) to calculate solvent-accessible surface area. BSA = SASA(unbound) - SASA(bound), representing the surface area buried upon binding.
Method: FreeSASA implements a rolling ball algorithm where a probe sphere (radius 1.4 Å, representing water) rolls over the protein surface to determine accessible areas.
| Parameter | Default Value | Description |
|---|---|---|
| Group A | - | First molecular group (multiple chains allowed) |
| Group B | - | Second molecular group (multiple chains allowed) |
| Distance Cutoff | 5.0 Å | Maximum distance to consider a residue as part of the interface (adjustable: 0.1-15.0 Å) |
| Calculate BSA | Yes (checked) | Enable/disable buried surface area calculation using FreeSASA |
| Color Scheme | Default | Options: Default, Heatmap (by BSA), Grouped (by chain) |
5.0 Å (default): Standard choice for most protein-protein interfaces. Captures direct contacts and some nearby interactions.
3.5-4.0 Å: Stricter definition, focuses on very close contacts only. Good for high-resolution structures.
6.0-8.0 Å: Broader definition, includes more peripheral residues. Useful for identifying extended binding regions.
Calculates pairwise distances between atoms or residues and visualizes spatial relationships between molecular groups.
Distance Calculation: Computes Euclidean distances between all atom pairs across the two selected groups. For residue-level distances, uses the minimum distance between any atoms of the two residues.
Formula: d = √[(x₂-x₁)² + (y₂-y₁)² + (z₂-z₁)²]
| Parameter | Default Value | Description |
|---|---|---|
| Group A | - | First group of chains |
| Group B | - | Second group of chains |
| Distance Cutoff | 5.0 Å | Maximum distance for network visualization (1.0-15.0 Å) |
| Visualization Type | All | Options: All (Dashboard), Heatmap, Network, or Histogram only |
| Color Scheme | Blue-Red | Options: Blue-Red gradient, Viridis, or Rainbow |
Color-coded interactive matrix showing pairwise distances between all residues. Red indicates close contacts, blue indicates distant pairs.
Graph representation where nodes are residues and edges connect residues within the cutoff distance. Edge thickness indicates proximity.
Distribution showing frequency of distances between groups. Helps identify characteristic separation distances.
Analyzes protein backbone and side-chain geometry to assess structure quality and conformational properties.
Ramachandran Angles: Calculates phi (φ) and psi (ψ) backbone dihedral angles for each residue. φ = C(-1) - N - Cα - C, ψ = N - Cα - C - N(+1). These angles define the conformational space accessible to the backbone.
Chi Angles: Measures side-chain torsion angles (χ₁, χ₂, χ₃, χ₄) depending on residue type. χ₁ = N - Cα - Cβ - Cγ (or first side-chain atom).
Bend Angles: Calculates the angle between consecutive Cα-Cα-Cα triplets to identify regions of backbone curvature. Bend angle = arccos[(b·c)/(|b||c|)]
| Parameter | Options | Description |
|---|---|---|
| Chains to Analyze | Multiple selection | Select which chains to include in geometry analysis |
| Visualization Type | All / Individual plots | Choose to see all geometry plots or specific ones (Ramachandran, Chi angles, Bend angles) |
Shows φ/ψ angle distribution for all residues. Most residues should fall in favored regions (α-helix, β-sheet). Outliers may indicate structural issues or unusual conformations.
Histograms showing side-chain rotamer preferences. Peaks correspond to commonly observed rotameric states.
Plot of bend angles along the sequence. High values indicate sharp turns or kinks; low values indicate straight segments.
The Ramachandran plot is an excellent quality indicator. Well-refined structures typically have >90% of residues in favored regions and <0.2% outliers (excluding Gly and Pro).
Calculates Solvent-Accessible Surface Area to determine how much of each residue is exposed to solvent vs. buried in the protein interior or interface.
Method: Implements the Lee & Richards (1971) rolling ball algorithm. A probe sphere (representing a water molecule) rolls over the van der Waals surface of the protein.
Calculation: The SASA is the surface traced by the center of the probe sphere. Areas accessible to the probe are considered exposed to solvent.
Bound vs Unbound: Calculates SASA for the complex (bound state) and for individual chains in isolation (unbound state). The difference reveals which areas become buried upon binding.
Formula: ΔSASA = SASA(unbound) - SASA(bound)
Burial Fraction = ΔSASA / SASA(unbound)
| Parameter | Default Value | Description |
|---|---|---|
| Chains to Analyze | All chains | Select specific chains or leave empty to analyze all. Note: Single chain selection won't calculate burial analysis. |
| Probe Radius | 1.4 Å | Radius of probe sphere (1.4 Å represents water molecule). Adjustable: 0.5-3.0 Å |
| Visualization Type | All | Options: All, Dashboard, Burial distribution, Bound/Unbound comparison, Heatmap, or Table only |
| SASA Method | FreeSASA | Calculation method (FreeSASA is default and recommended) |
Histogram showing how many residues have different burial fractions. Interface residues typically show 50-100% burial.
Bar chart comparing SASA values in complex vs. isolated state for each chain.
Color-coded visualization of SASA values for each residue along the sequence.
Detailed spreadsheet listing all interface residues with their SASA values, burial fractions, and residue types.
0-20% buried: Surface-exposed residues, minimal involvement in interface
20-50% buried: Partially buried, peripheral interface residues
50-80% buried: Significant burial, core interface residues
80-100% buried: Highly buried, key binding residues or internal protein core
VDW energy calculation is computationally intensive and can take 3-5 minutes for large structures. This analysis is optional and recommended only when detailed energy information is needed.
Calculates van der Waals interaction energies between atoms to identify energetically favorable contacts and binding hotspots.
Formula: Uses the AMBER 12-6 Lennard-Jones potential:
EVDW = ε[(rmin/r)12 - 2(rmin/r)6]
Where:
Interpretation:
Parameters: Uses AMBER force field parameters for atomic radii and well depths for each atom type.
| Parameter | Default Value | Description |
|---|---|---|
| Group A (Receptor) | - | First molecular group (e.g., antibody) |
| Group B (Ligand) | - | Second molecular group (e.g., antigen) |
| Distance Cutoff | 5.0 Å | Maximum distance for VDW calculation (3.0-10.0 Å). Larger cutoffs increase computation time significantly. |
| Energy Threshold | -2.0 kcal/mol | Minimum energy to identify as hotspot (-10.0 to 0.0 kcal/mol). More negative = stronger interactions only. |
| Ignore Hydrogen | Yes (checked) | Skip hydrogen atoms for faster calculation (recommended) |
| Show 3D Viewer | Yes (checked) | Include interactive 3D visualization of energies |
| Top N Hotspots | 20 | Number of strongest interactions to highlight (5-50) |
| 3D Viewer Size | Medium | Options: Small (600×450), Medium (800×600), Large (1000×750) |
-2.0 kcal/mol (default): Identifies moderately strong interactions, good starting point
-1.0 kcal/mol: More inclusive, captures weaker interactions
-3.0 to -5.0 kcal/mol: Very selective, only strongest hotspots
Tip: Start with default -2.0 and adjust based on results. Very negative thresholds may return few or no interactions.
VDW analysis is particularly useful for identifying binding hotspots for drug design, predicting mutation effects on binding affinity, and understanding the energetic basis of protein-protein recognition.
Compare multiple variants of protein-protein complexes side-by-side to identify structural differences, analyze mutation effects, and understand sequence-structure-function relationships.
Upload 2 or more PDB files. Each structure should be given a unique variant name (e.g., WT, V1, V2, Y53F).
Select one structure as the Wild-Type (WT) reference. All other variants will be compared against this reference.
Group chains into functional categories (e.g., "antibody" = chains H,L; "antigen" = chain A). This enables group-level analysis.
SPICE calculates comprehensive properties across all structures and generates an interactive dashboard.
| Property | Description |
|---|---|
| Contact Counts | Number of each contact type (H-bonds, salt bridges, etc.) for each variant |
| Interface Areas | Buried surface area (BSA) and interface size for each complex |
| Contact Differences | Contacts lost or gained relative to WT |
| Geometry Metrics | Backbone and side-chain angles distribution |
| VDW Metrics | VDW energy distribution across all residues |
| Statistical Summary | Mean, standard deviation, and trends across all variants |
The multi-complex dashboard provides:
Structure Alignment: All variants must be structurally aligned to the WT reference using Cα atom superposition before comparison.
Property Calculation: Each variant undergoes the same analysis pipeline (contacts, interface, SASA, etc.) with identical parameters.
Statistical Comparison: Properties are normalized and compared using difference scores and percentage changes relative to WT.
For multi-chain analysis, residues are displayed sequentially with vertical lines marking chain boundaries. Each variant is shown in a different color, making it easy to compare values across the entire complex.
Color-coded matrices showing property differences between variants and WT. Red indicates increase, blue indicates decrease.
Antibody Engineering: Compare antibody variants with different CDR mutations to optimize affinity and specificity.
Disease Mutations: Analyze how disease-associated mutations affect protein structure and interactions.
Rational Design: Guide protein engineering by identifying which properties change with specific mutations.
After analysis completes, you'll see an organized results page with:
| Format | Best For | Contains |
|---|---|---|
| HTML Report | Presentations, sharing with collaborators | All visualizations and tables, interactive |
| PNG Images | Publications, posters | High-resolution static images of plots |
| CSV Files | Further analysis in Excel, R, Python | Raw data tables in spreadsheet format |
Session Isolation: Your results are stored in a session-specific folder. They will be cleared when you close your browser or clear the session.
Download Results: Always download important results before closing your browser or starting a new analysis.
A: The progress indicator will disappear and the results page will automatically load. You'll see "Analysis Complete" at the top of the page.
A: Yes! Click "Run Another Analysis" to return to the parameter selection page. Your structure will remain loaded.
A: First verify your parameter selections (cutoff distances, chain selections). Check that you selected the correct chains for Group A and Group B. Review the algorithm details in this guide for interpretation.
A: Results persist for your current browser session. They're automatically cleared when you close your browser, start a new session, or manually clear your session.