i3Drefine

i3Drefine refines protein three-dimensional structures by iteratively optimizing hydrogen-bonding networks and performing atomic-level energy minimization using composite physics and knowledge-based force fields to improve structural quality for modeling and analysis.

Key Features:

• Iterative Optimization: Employs an iterative protocol that optimizes hydrogen-bonding networks and applies atomic-level energy minimization to adjust local and global structural features.
• Composite Force Fields: Integrates composite physics and knowledge-based force fields for energy evaluation and refinement.
• Statistical and Visual Analysis: Provides energy and statistical feedback and enables interactive visualization of multiple refined models via the JSmol applet.
• Extensive Validation: Validated in blind CASP experiments and on large-scale diverse benchmark datasets, demonstrating consistent improvement over initial models.

Scientific Applications:

• Protein Model Improvement: Improves predicted and experimentally determined protein models to increase accuracy of three-dimensional structures.
• Structure-Based Drug Design: Produces refined models suitable for structure-based drug design and computational chemistry analyses.
• Functional and Mechanistic Studies: Supports interpretation of protein function and molecular mechanisms through enhanced local and global structural quality.

Methodology:

Uses an iterative refinement protocol that optimizes hydrogen-bonding networks and performs atomic-level energy minimization with composite physics and knowledge-based force fields.