DINC

DINC implements an incremental docking protocol to enable accurate and efficient docking of large ligands (those with more than six rotatable bonds) using AutoDock.

Key Features:

• Incremental Docking Protocol: Breaks the docking of large ligands into smaller increments rather than docking the full ligand in a single step to improve accuracy and computational efficiency.
• Positional Restraints: Supports application of positional restraints during docking to provide additional control over docked conformations of large ligands.
• Benchmark Performance: Demonstrated on 73 protein–ligand complexes with large ligands, reporting up to two orders of magnitude speed increase compared to AutoDock's standard protocol without compromising docking accuracy.

Scientific Applications:

• Therapeutic Drug Design: Enables improved modeling and optimization of large ligand–protein interactions relevant to small-molecule drug discovery.
• Rational Vaccine Development: Facilitates modeling of large molecular complexes that may inform vaccine antigen or adjuvant design.
• Modeling Complex Molecular Interactions: Provides an approach for studying conformations and binding modes of large ligands in protein–ligand complexes.

Methodology:

Implements an incremental docking strategy that breaks large ligands into smaller increments and docks them using AutoDock, supports positional restraints, and was benchmarked on 73 protein–ligand complexes reporting up to two orders of magnitude speed improvement.