GOMoDo

GOMoDo performs structural modeling and ligand docking of G-protein coupled receptors (GPCRs) to predict three-dimensional receptor structures and ligand–receptor binding interactions.

Key Features:

• Integrated pipeline: Combines template selection, homology modeling, binding pocket prediction, structural alignment, and ligand docking into a single computational workflow.
• Template selection (HHsearch 1.5.1): Identifies suitable GPCR templates using the HHsearch package version 1.5.1 for sequence alignment-based template selection.
• Homology modeling (Modeller 9.20): Builds three-dimensional GPCR models using Modeller version 9.20.
• Binding pocket prediction (FPOCKET): Predicts potential ligand-binding pockets on GPCR models using FPOCKET.
• Ligand docking (Autodock VINA, HADDOCK): Performs ligand docking with Autodock VINA or HADDOCK and supports both blind and information-driven docking strategies.
• Structural alignment (LOVOALIGN): Uses LOVOALIGN to perform structural alignment of models for precise orientation prior to VINA docking.

Scientific Applications:

• GPCR structure prediction: Produces comparative models of GPCR sequences to infer three-dimensional receptor structures.
• Ligand binding mode prediction: Predicts ligand binding modes and interactions through Autodock VINA or HADDOCK docking simulations.
• Binding site identification: Identifies and ranks putative binding pockets on modeled GPCR structures using FPOCKET.
• Structure-based drug discovery: Supports computational studies and virtual screening efforts targeting GPCRs using modeled structures and docking results.

Methodology:

Template selection is performed with HHsearch v1.5.1, homology models are built with Modeller v9.20, binding pockets are predicted with FPOCKET, structural alignments for VINA docking use LOVOALIGN, and ligand docking is carried out with Autodock VINA or HADDOCK.