Frog

Frog generates three-dimensional (3D) conformations of drug-like compounds from one-dimensional (SMILES) or two-dimensional (SDF) representations for use in computational drug discovery.

Key Features:

• Input Formats: Accepts SMILES and SDF input formats.
• Conformation Generation: Generates 3D conformations using atomic constitution and connectivity information.
• Isomer Identification: Identifies unambiguous isomers corresponding to each compound.
• Energy Consideration: Produces single or multiple low-to-medium energy 3D models focusing on energetically favorable conformations.
• Ring Treatment: Does not account for ring flexibility during the assembly process and focuses on rigid-body conformation generation.
• Validation and Accuracy: Can generate conformations closely resembling those observed in crystallographic complexes.

Scientific Applications:

• Ligand-based screening: Supplies multiple conformers per ligand for ligand-based screening computations.
• Structure-based screening and docking: Supports hierarchical structure-based screening projects that involve rigid-body docking steps by providing conformers for docking.

Methodology:

Generates 3D conformations from SMILES or SDF by using atomic constitution and connectivity information, identifying unambiguous isomers, and assembling rigid-body low-to-medium energy 3D models; ring flexibility is not modeled.