RAPIDO

RAPIDO: Structural alignment of protein rigid-body atom groups

RAPIDO performs structural alignment of protein structures by identifying groups of equivalent atoms defined as rigid bodies based on conserved interatomic distances within a specified tolerance. It detects structurally equivalent regions, including sequence-distant fragments separated by flexible domains, and outputs residue sets suitable for accurate structural superposition.

Key Features:

• Rigid-Body Atom Group Identification: Defines equivalent atom groups using constancy of interatomic distances within a specified tolerance between compared protein structures.
• Non-Contiguous Region Recognition: Aligns structurally equivalent regions that are distant in sequence and separated by flexible domains.
• B-Value Weighting Functions: Incorporates weighting based on refined B-values to account for variability in atomic coordinate reliability during distance comparisons.
• Residue Set Output: Generates reliable residue sets enabling accurate superposition of two protein structures.

Scientific Applications:

• Protein Structural Analysis: Supports investigation of protein function, conformational changes associated with ligand binding or enzymatic activity, and evolutionary relationships through comparative structural analysis.

Methodology:

RAPIDO applies a structural alignment algorithm that detects equivalent atoms by evaluating interatomic distance conservation within a defined tolerance. Equivalent atoms are grouped into rigid bodies, including non-contiguous sequence fragments. Distance comparisons are weighted using refined B-values to incorporate coordinate reliability, and resulting residue sets are used for structural superposition.