Using HBAT Web

Using HBAT Web#

HBAT Web provides an interactive web-based interface for analyzing hydrogen bonds and other molecular interactions in protein structures. The web interface is available at hbat-web.abhishek-tiwari.com.

Features#

The HBAT Web interface provides:

  • File Upload: Load PDB or mmCIF structure files

  • Interactive Analysis: Configure analysis parameters and run interactions detection

  • Tabbed Results: View results organized by interaction type

  • Search & Filter: Filter results by residue, interaction type, or distance

  • 3D Visualization: Visualize interactions in 3D using 3Dmol.js and PyMol

  • Data Export: Export analysis results in multiple formats

  • Real-time Processing: Automatic analysis on file upload or parameter changes

Getting Started#

HBAT Web analysis follows a 4-stage workflow:

  1. Upload PDB File - Load your structure

  2. Configure Parameters & Run - Set analysis options

  3. View Results - Examine interactions detected

  4. Export Results - Save your analysis data

1. Upload PDB File#

  • Option 1: Upload Structure File from local computer or

  • Option 2: Download from RCSB PDB by entering a valid PDB ID

The file will be automatically processed and displayed.

The interface supports:

  • PDB Format (.pdb): Protein Data Bank standard format

  • mmCIF Format (.cif): Crystallographic Information File format

Click Next.

2. Configure Parameters & Run#

After uploading a PDB file:

PDB Fixing Parameters:

  • Fix PDB: Enable PDB fixing (adds missing atoms/hydrogens)

  • Fixing Method: Choose between OpenBabel or PDBFixer

  • Analysis Mode: Complete (all interactions) or Local (intra-residue only)

Hydrogen Bond Parameters:

  • H…A Distance Cutoff (Å)

  • D-H…A Angle Cutoff (degrees)

  • Donor-Acceptor Distance Cutoff (Å)

Halogen Bond Parameters:

  • X…A Distance Cutoff

  • C-X…A Angle Cutoff

π Interaction Parameters:

  • H…π Distance Cutoff

  • D-H…π Angle Cutoff

π-π Stacking Parameters:

  • Centroid-to-Centroid Distance

  • Parallel Angle Range

  • T-shaped Angle Range

  • Lateral Offset

Carbonyl & n-π* Parameters:

  • Distance and angle thresholds for each interaction type

n→π* Interactions:

  • Distance and angle thresholds for lone pair to π interactions

General Settings:

  • Analysis mode (Complete vs Local)

Click Analyze to run the analysis with the configured parameters.

3. View Results#

The central area displays analysis results organized in tabs:

  • Summary: Overview of all interactions detected

  • Hydrogen Bonds: H-bonds with donor/acceptor information

  • Halogen Bonds: Halogen bonding interactions

  • π Interactions: π-system interactions

  • π-π Stacking: Aromatic ring stacking

  • Carbonyl Interactions: n→π* interactions

  • n-π* Interactions: Lone pair to π interactions

  • Water Bridges: Water-mediated hydrogen bond networks

  • Ligand Interactions: Interactions involving ligands

  • Cooperativity Chains: Hydrogen bond networks and cooperativity

Each tab contains:

  • Data Table: Searchable results with columns for residue information, distances, and angles

  • Search Bar: Filter results by residue, atom name, or distance value

Searching Results#

Each interaction tab includes a search field:

  1. Type a search term in the filter field (e.g., “ARG”, “A:ASP:42”)

  2. Click Filter to show matching results

  3. Click Clear to show all results

  4. Search is case-insensitive and matches partial strings

Working with Ligands#

When a structure contains ligands:

  1. The Ligand Interactions tab becomes active

  2. Use the ligand selector dropdown to filter by specific ligand

  3. View two tables:

    • Regular Interactions: Direct protein-ligand interactions

    • Water Bridges: Water-mediated ligand interactions

Visualizing Interactions#

For supported interactions, click on a row in the results table to view a 3D visualization:

  1. The py3Dmol viewer shows the structure with the interaction highlighted

  2. Interacting residues are colored differently (cyan/orange)

  3. Interaction distance is displayed as a dashed line

  4. Use your mouse to rotate, zoom, and pan the structure

  5. Click Export as PNG to save the visualization

Click Next to export results or `Back` to go back re-analyze structure with different parameters.

4. Export Results#

After analyzing your structure, export the results for further analysis or documentation.

Export analysis results in multiple formats:

Text Format (.txt):

  • Human-readable summary with all interactions listed

  • Includes timing information and parameter settings

JSON Format (.json):

  • Complete structured data in JSON format

  • Suitable for programmatic processing

  • Contains all interaction details and metadata

CSV Format (.csv):

  • Tabular format for spreadsheet applications

  • Separate files for each interaction type

  • Easy to process in Excel or data analysis tools

To export:

  1. Choose your preferred format (Text, JSON, or CSV)

  2. The file will be downloaded to your computer

Tips & Best Practices#

PDB Fixing

  • Enable PDB fixing for structures with missing atoms or hydrogens

  • Choose OpenBabel for most cases (faster, more accurate)

  • PDBFixer is useful for complex structures with special requirements

Parameter Tuning

  • Start with preset values (see Analysis Parameters Guide)

  • Adjust distance cutoffs first when troubleshooting missing interactions

  • For drug design work, use stricter angle thresholds

  • For structure validation, use looser criteria

Large Structures

  • Web interface handles structures with up to ~10,000 atoms efficiently

  • Analysis usually completes in seconds

  • Larger structures may take longer to visualize in 3D

Saving Your Work

  • Always export results to file for permanent storage

  • Export before closing the browser tab

  • Results are lost when the page is refreshed

  • Keep exported files for downstream analysis

Troubleshooting#

“Invalid file format”

  • Ensure file is valid PDB or mmCIF format

  • Check file extension (.pdb or .cif)

  • Try downloading the structure from PDB directly

  • Reduce distance cutoffs (structures may need relaxed criteria)

  • Ensure PDB fixing is enabled if structure has missing atoms

  • Verify structure contains expected protein elements

  • Large structures (>50,000 atoms) may take longer

  • Try enabling PDB fixing to standardize the structure

  • Reduce the number of interaction types analyzed

  • Check browser console for errors

  • Ensure JavaScript is enabled

  • Try a different browser (Chrome, Firefox, Safari recommended)

  • Clear browser cache and reload

Performance Considerations#

The HBAT Web interface is optimized for:

  • Typical protein structures (1,000 - 10,000 atoms)

  • Standard analysis parameters

  • Real-time interactive use

For very large structures or batch processing:

Getting Help#

For more information: