domains / families / science / geometric-analysis

geometric-analysis

separate

Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD, center of mass, radius of gyration, and solvent accessible surface area (SASA). Use when deciding that RMSD depends on BOTH the superposition and the atom selection (a global all-atom RMSD is dominated by flexible loops and hinge motion and is NOT a cross-protein similarity metric); choosing the metric that matches the question (RMSD for same-molecule displacement, TM-score for same-fold, lDDT for superposition-free local model quality - the quantity pLDDT predicts); recognizing Superimposer needs an equal-length ordered atom-to-atom correspondence; and reporting SASA only alongside its probe radius (1.4A water, Shrake-Rupley) with a preference for relative SASA. Keywords RMSD, TM-score, lDDT, SASA, Shrake-Rupley, superposition, Kabsch, dihedral, Ramachandran, radius of gyration.

When to use

• interatomic distances
• distance matrices
• bond and dihedral angles
• Ramachandran analysis
• superposition and RMSD
• center of mass
• radius of gyration
• solvent accessible surface area (SASA)

When not to use

• cross-protein similarity metrics
• structure-based alignment
• interpreting Ramachandran outliers as quality flags

Skill page

Source