Molecular Docking Nodes
Complete molecular docking workflow with AutoDock Vina integration, GPU acceleration, and comprehensive analysis tools for drug discovery.
Node Reference
Detailed documentation for each molecular docking node available in VERA.
AutoDock Vina
CPU-based molecular docking using AutoDock Vina with batch processing support
Key Features
- •Batch docking support for multiple ligands
- •Automatic RDKit to PDB to PDBQT conversion
- •Automatic receptor rigidification for Vina compatibility
- •Multiple Vina versions with automatic resolution
- •Grid parameters can be provided via input or properties
- •Aggregated results across all ligands with naming
- •Concatenated logs for debugging and analysis
- •Hydrogen management and conformer processing
Input Ports
Receptor protein structure (RDKit mol)
Ligand molecules for docking (RDKit mol list)
Optional grid parameters dictionary
Output Ports
DataFrame with docking scores, RMSD values, and ligand names
All poses as RDKit molecules
Best scoring pose as single molecule
Raw docking log text for all ligands
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| center_x | float | 0.0 | Grid center X coordinate (Angstroms) |
| center_y | float | 0.0 | Grid center Y coordinate (Angstroms) |
| center_z | float | 0.0 | Grid center Z coordinate (Angstroms) |
| size_x | float | 20.0 | Grid size X dimension (Angstroms) |
| size_y | float | 20.0 | Grid size Y dimension (Angstroms) |
| size_z | float | 20.0 | Grid size Z dimension (Angstroms) |
| exhaustiveness | int | 8 | Search exhaustiveness (higher = more thorough) |
| num_modes | int | 9 | Number of binding modes to generate |
| energy_range | float | 3.0 | Energy range cutoff for poses (kcal/mol) |
| vina_version | string | 1.2.5 | Vina version to use (1.1.2, 1.2.3-1.2.7) |
AutoDock Vina GPU
GPU-accelerated molecular docking using AutoDock Vina GPU with CUDA optimization
Key Features
- •CUDA acceleration for high-throughput virtual screening
- •Automatic GPU executable resolution
- •Batch processing optimization for GPU
- •Thread configuration for performance tuning
- •Same interface as CPU version for easy switching
- •Optimized for NVIDIA GPUs with CUDA support
- •Maintained compatibility with standard Vina parameters
Input Ports
Receptor protein structure (RDKit mol)
Ligand molecules for docking (RDKit mol list)
Optional grid parameters dictionary
Output Ports
DataFrame with docking scores, RMSD values, and ligand names
All poses as RDKit molecules
Best scoring pose as single molecule
Raw docking log text for all ligands
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| center_x | float | 0.0 | Grid center X coordinate (Angstroms) |
| center_y | float | 0.0 | Grid center Y coordinate (Angstroms) |
| center_z | float | 0.0 | Grid center Z coordinate (Angstroms) |
| size_x | float | 20.0 | Grid size X dimension (Angstroms) |
| size_y | float | 20.0 | Grid size Y dimension (Angstroms) |
| size_z | float | 20.0 | Grid size Z dimension (Angstroms) |
| exhaustiveness | int | 8 | Search exhaustiveness (inherited from CPU version) |
| num_modes | int | 9 | Number of binding modes to generate |
| energy_range | float | 3.0 | Energy range cutoff for poses (kcal/mol) |
| gpu_batch | int | 50 | GPU batch size for processing |
| thread | int | 1000 | Thread count per GPU block |
Receptor Preparation
Prepare protein receptor for docking (PDB/PDBQT conversion)
Key Features
- •Automatic hydrogen addition
- •Water molecule removal
- •Missing atom repair
- •Format conversion handling
Input Ports
Receptor file (PDB/PDBQT)
Or RDKit molecule
Output Ports
Prepared receptor molecule
Receptor PDBQT file path
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| add_hydrogens | bool | true | Add missing hydrogens |
| remove_water | bool | true | Remove water molecules |
| fix_residues | bool | true | Fix missing atoms in residues |
Ligand Preparation
Prepare ligands for docking with charge and torsion assignment
Key Features
- •Gasteiger charge calculation
- •Rotatable bond detection
- •3D structure generation if needed
- •Batch processing support
Input Ports
Ligand file (SDF/MOL/MOL2)
Or RDKit molecules
Output Ports
Prepared ligand molecules
Ligand PDBQT file paths
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| add_hydrogens | bool | true | Add hydrogens |
| compute_charges | bool | true | Compute Gasteiger charges |
| detect_torsions | bool | true | Detect rotatable bonds |
Grid Search
Define and optimize docking grid box parameters
Key Features
- •Automatic grid centering
- •Reference ligand-based positioning
- •Active site detection
- •Visual grid preview
Input Ports
Receptor structure
Optional reference ligand for centering
Output Ports
Grid parameters dictionary
Grid box visualization
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| method | string | center_of_mass | Grid centering method |
| padding | float | 10.0 | Padding around reference |
| spacing | float | 0.375 | Grid spacing (Angstroms) |
Docking Analysis
Analyze and visualize docking results
Key Features
- •Binding affinity analysis
- •RMSD-based pose clustering
- •Interaction fingerprinting
- •Statistical summaries
- •Publication-ready plots
Input Ports
Docking results DataFrame
Docked poses
Receptor structure
Output Ports
Detailed analysis DataFrame
Protein-ligand interactions
Pose clustering analysis
Analysis plots
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| rmsd_threshold | float | 2.0 | RMSD clustering threshold |
| energy_cutoff | float | -6.0 | Binding energy cutoff |
| analyze_interactions | bool | true | Analyze molecular interactions |
Vina Split
Split multi-model PDBQT files from docking results
Key Features
- •Multi-model PDBQT parsing
- •Individual pose extraction
- •Energy score extraction
- •Batch file splitting
Input Ports
Multi-model PDBQT file
Or docked molecules
Output Ports
Individual pose molecules
Individual PDBQT files
Pose information DataFrame
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| max_poses | int | 9 | Maximum poses to extract |
| vina_version | string | auto | Vina version for compatibility |
Merge Molecule
Combine receptor and ligand into single complex structure
Key Features
- •Protein-ligand complex creation
- •Multi-ligand support
- •Format preservation
- •Chain ID management
Input Ports
Receptor structure
Ligand structure(s)
Output Ports
Merged complex structure
Complex PDB file
Properties
| Property | Type | Default | Description |
|---|---|---|---|
| output_format | string | pdb | Output file format |
| combine_method | string | append | Molecule combination method |
Workflow Examples
Common molecular docking workflows you can build with these nodes.
Basic Molecular Docking
Simple receptor-ligand docking workflow
- 1Load receptor PDB file using File Input node
- 2Prepare receptor with Receptor Preparation node
- 3Load ligand SDF file using SDF Reader node
- 4Prepare ligands with Ligand Preparation node
- 5Connect to AutoDock Vina node
- 6Analyze results with Docking Analysis node
- 7Visualize with Web 3D Viewer node
High-Throughput Virtual Screening
Screen large compound library with GPU acceleration
- 1Load receptor structure
- 2Define grid with Grid Search node
- 3Load compound library (SDF/CSV)
- 4Prepare ligands in batch
- 5Use AutoDock Vina GPU for screening
- 6Filter by binding energy threshold
- 7Cluster similar poses
- 8Export top hits to CSV
Structure-Based Drug Design
Iterative docking with interaction analysis
- 1Load crystal structure complex
- 2Extract reference ligand
- 3Generate grid from reference
- 4Dock analogs with Vina
- 5Analyze interactions with ProLIF
- 6Compare interaction fingerprints
- 7Visualize binding modes
- 8Select leads for optimization