ZDOCK

ZDOCK performs rigid-body docking to predict structures of protein-protein complexes and symmetric multimers using exhaustive orientation searches and statistical scoring.

Key Features:

• Rigid-Body Docking: Performs a comprehensive full rigid-body search of docking orientations between two proteins.
• M-ZDOCK (symmetric multimer docking): Extends docking to symmetric multimers using the M-ZDOCK algorithm.
• Pairwise Statistical Energy Potential: Employs a pairwise statistical energy potential to score and rank docking conformations.
• Performance Optimization: Incorporates performance optimization techniques to enhance computational efficiency during exhaustive searches.
• Scoring and Output Selection: Generates and scores numerous possible orientations and supports selection of output models based on scoring criteria.

Scientific Applications:

• Protein–Protein Complex Prediction: Predicts structures of protein-protein complexes when experimental complex structures are unavailable.
• Symmetric Multimer Modeling: Models symmetric multimers to characterize oligomeric assembly interfaces.
• Mechanistic Studies: Supports investigation of molecular mechanisms underlying cellular and immune functions by providing structural hypotheses for interactions.

Methodology:

Uses the rigid-body docking programs ZDOCK and M-ZDOCK to generate and score numerous possible orientations of interacting proteins using a pairwise statistical energy potential, and allows influence over scoring criteria and selection of output models.