StarMap

StarMap refines 3D atomic models of biological macromolecules into cryogenic electron microscopy (cryo-EM) density maps to improve model fit and assess structural accuracy.

Key Features:

• Monte Carlo sampling: Uses Monte Carlo sampling to explore conformational space for alternative model conformations.
• Local density-guided optimization: Applies local density-guided optimization to improve model fit to cryo-EM maps.
• Rosetta-based all-atom refinement: Performs all-atom refinement using the Rosetta molecular modeling engine.
• Real-space B-factor calculation: Calculates real-space B-factors to assess local model flexibility and accuracy.
• Symmetry adjustments: Implements structural symmetry adjustments for symmetric assemblies.
• Local refinements and independent validation: Supports local refinement procedures and independent model validation workflows.
• Magnification (pixel size) calibration: Performs magnification/pixel size calibration for accurate map scaling.
• Fourier shell correlation (FSC) analysis: Computes Fourier shell correlations for resolution and fit assessment.
• Per-residue Z-scores: Produces per-residue Z-scores as interpretable metrics for goodness of fit and for identifying flexible or potentially functional sites.

Scientific Applications:

• Model refinement and validation: Refinement and validation of atomic models into cryo-EM density maps using quantitative metrics such as FSC and per-residue Z-scores.
• Protein dynamics and flexibility analysis: Characterization of local flexibility and conformational variability using real-space B-factors and Z-scores.
• Functional site identification and structure-guided design: Identification of flexible or functionally relevant regions to inform studies of interactions and structure-guided drug design.

Methodology:

Performs Monte Carlo sampling, local density-guided optimization, Rosetta-based all-atom refinement, real-space B-factor calculation, magnification (pixel size) calibration, Fourier shell correlation computation, structural symmetry adjustments, local refinements, independent model validations, and per-residue Z-score calculation.