RosettaDock Server

RosettaDock Server predicts low-energy conformations of protein-protein complexes by sampling rigid-body orientations and side-chain conformations from a provided starting configuration to identify energetically favorable binding structures.

Key Features:

• Input requirements: Accepts two protein structures and a specified starting location for the docking search.
• Conformational sampling: Optimizes both rigid-body orientations and side-chain conformations during docking.
• Model generation: Produces 1000 independent structural models of the interacting proteins for conformational exploration.
• Scoring and selection: Scores models by total energy and returns the top 10 scoring models with coordinate files and scoring information.
• Energy landscape analysis: Plots the total energy of all generated models to evaluate the presence or absence of an energetic binding funnel.
• Validation: Performance has been evaluated on established docking benchmark sets and in CAPRI blind prediction challenges.

Scientific Applications:

• Protein–protein docking prediction: Predicts plausible bound conformations and interfaces for protein complexes.
• Structural biology: Aids atomic-level interpretation of molecular recognition by sampling side-chain and rigid-body rearrangements.
• Hypothesis testing: Provides scored model ensembles and energy funnels to support evaluation of binding hypotheses and interface stability.

Methodology:

Optimizes the spatial arrangement of two interacting proteins by sampling rigid-body orientations and side-chain conformations to minimize total energy, generates 1000 independent models, scores them by energy, returns the top 10 models, and plots the total energy distribution to assess binding funnels.