Bioshift provides comprehensive molecular docking capabilities through AutoDock Vina integration, supporting both CPU and GPU-accelerated versions for drug discovery and virtual screening applications.
Comprehensive molecular docking with multiple Vina versions and GPU acceleration.
Multiple Vina versions (1.1.2, 1.2.3-1.2.7) included
GPU acceleration with Vina GPU 2.1 (CUDA)
Automated receptor and ligand preparation
Batch docking for virtual screening
Grid search optimization
Result analysis and visualization
Original AutoDock Vina version
Updated scoring function
Latest stable CPU version
GPU-accelerated for high-throughput
Standard molecular docking workflow from receptor preparation to result analysis.
Convert protein structure to PDBQT format
Prepare ligands with charges and torsions
Define search box around binding site
Run molecular docking simulation
Analyze binding poses and scores
View protein-ligand complexes
Key parameters for defining the docking search space.
| Parameter | Description | Default Value |
|---|---|---|
| center_x, center_y, center_z | Grid box center coordinates (Å) | Calculated from ligand or pocket |
| size_x, size_y, size_z | Grid box dimensions (Å) | 20 × 20 × 20 |
| exhaustiveness | Search thoroughness | 8 (higher = more thorough) |
| num_modes | Number of binding poses | 9 |
| energy_range | Energy range for poses (kcal/mol) | 3.0 |
Performance comparison for virtual screening of compound libraries.
| Library Size | CPU Time (Vina 1.2.5) | GPU Time (Vina GPU 2.1) | Speedup |
|---|---|---|---|
| 10 compounds | 5 min | 30 sec | 10x |
| 100 compounds | 50 min | 2 min | 25x |
| 1,000 compounds | 8 hours | 15 min | 32x |
| 10,000 compounds | 3 days | 2 hours | 36x |
| 100,000 compounds | 30 days | 20 hours | 36x |
* Performance may vary based on hardware, protein size, and docking parameters.
Recommendations for optimal docking results.