STON

STON identifies aligned residues between two protein structures using a user-specified root mean square deviation (RMSD) threshold to detect local structural similarities relevant to evolutionary and functional analysis.

Key Features:

• Residue-level alignment: Identifies aligned residues between two protein structures according to an RMSD criterion.
• Parameterized Distance and Rotation: Allows adjustment of distance and rotation parameters to detect both strongly and weakly similar aligned fragments.
• Desired RMSD Value Alignment: Enables specification of an RMSD threshold instead of minimizing RMSD to capture a broader range of biologically relevant alignments.

Scientific Applications:

• Structural Genomics: Aids comparative analysis of protein structures by identifying local alignments at specified RMSD values.
• Functional Genomics: Supports detection of local structural similarities that inform protein function and evolutionary relationships.

Methodology:

The algorithm focuses on finding alignments that satisfy a user-specified RMSD threshold rather than solely minimizing RMSD and uses adjustable distance and rotation parameters.