ModRefiner

ModRefiner refines protein structures by reconstructing main-chain and side-chain atoms from Cα traces and performing atomic-level energy minimization to improve local and global structural accuracy for structural biology analyses.

Key Features:

• Starting Models: Accepts Cα traces, main-chain models, or complete atomic models as input for refinement.
• Two-Step Energy Minimization: Employs a two-step process where main-chain structures are constructed from Cα traces and then side-chain rotamers together with backbone atoms are refined using a composite force field integrating physics-based and knowledge-based components.
• Flexibility in Simulations: Allows full flexibility of both side-chain and backbone atoms during refinement simulations to explore conformational space guided by the composite force field.
• Benchmark Performance: Validated on 261 proteins from ab initio and template-based initial models, reporting improvements in global and local structural accuracy, side-chain positions, hydrogen-bonding networks, and reduced atomic overlaps compared with other programs.

Scientific Applications:

• Detailed Function Analysis: Enables construction of accurate full-atom models from reduced representations for detailed analysis of protein function and interactions.
• Validation and Refinement: Serves to validate and refine predicted protein structures while preserving correct global topology and improving local atomic geometry.

Methodology:

Performs a two-step computational protocol: (1) main-chain construction from Cα traces, and (2) simultaneous side-chain rotamer and backbone refinement via atomic-level energy minimization using a composite physics-based and knowledge-based force field with full side-chain and backbone flexibility.