MolFit

MolFit performs rigid-body docking by representing molecules as three-dimensional grids of complex numbers and correlating these grids to estimate geometric and chemical surface complementarity.

Key Features:

• High Sensitivity: Produces sensitive docking solutions that remain reasonably accurate for structures undergoing moderate local conformational changes or for modeled structures.
• Rigid-Body Docking: Operates under a rigid-body assumption where molecules do not change shape during docking and can incorporate external biochemical or bioinformatic data to guide docking.
• Multibody Multistage Docking: Employs a rigid multibody multistage docking procedure to accommodate large global conformational changes, including domain movements.
• Ranking Challenges: Experiences challenges in ranking docking solutions, particularly for NMR or modeled structures when external data do not favor a single solution.

Scientific Applications:

• CAPRI protein–protein interaction prediction: Applied in CAPRI (Critical Assessment of PRediction of Interactions) experiments for predicting protein–protein interactions.
• Modeling conformational and multibody assemblies: Used to model complexes with moderate local conformational changes and multibody assemblies that involve domain movements.

Methodology:

Represents molecules as three-dimensional grids of complex numbers; correlates these grids to estimate geometric and chemical surface complementarity; applies rigid-body docking and a rigid multibody multistage docking procedure; uses external biochemical or bioinformatic data to guide docking and performs ranking of docking solutions (ranking selectivity may require readjustment).