MDock

MDock performs molecular inverse docking and target prediction to identify potential protein targets and evaluate binding affinities of small molecules using a knowledge-based scoring function (ITScore).

Key Features:

• Ensemble Docking Algorithm: Performs docking of ligands against multiple protein structures or conformations to account for protein structural variability.
• Knowledge-Based Scoring Function (ITScore): Uses the ITScore knowledge-based scoring function to evaluate protein–ligand binding affinities.
• Inverse Docking Capability: Predicts potential protein targets for specified molecules to support target identification and repurposing studies.
• Computational Efficiency: Enables rapid processing of docking simulations for large datasets and complex protein–ligand systems.

Scientific Applications:

• Drug Repurposing: Identifies new therapeutic targets for existing compounds by predicting potential protein interactions.
• Off-Target and Toxicity Prediction: Supports early-stage identification of potential side effects through prediction of off-target protein interactions.
• Structural Dynamics and Lead Identification: Explores protein–ligand interactions across multiple conformations to inform lead compound selection.

Methodology:

MDock performs ensemble docking by optimizing ligands against single protein structures or ensembles of structures and computes protein–ligand complex scores using the knowledge-based ITScore scoring function.