STRIDE

STRIDE assigns secondary structure to atomic-resolution protein structures using a knowledge-based algorithm that combines hydrogen-bond energy and backbone torsional angle statistics.

Key Features:

• Secondary Structure Assignment: Assigns detailed secondary structure labels from atomic coordinates of protein structures.
• Knowledge-Based Algorithm: Integrates hydrogen-bond energy calculations with statistically derived backbone torsional angle information.
• Contact and Ramachandran Maps: Produces contact maps and Ramachandran plots derived from atomic coordinates.
• PDB Format Support: Operates on atomic coordinates provided in Protein Data Bank (PDB) format.
• Concordance with Crystallographers: Generates assignments that align closely with secondary-structure designations made by crystallographers.

Scientific Applications:

• Protein Structure Analysis: Supports analysis of protein folding, stability, and structural annotation through secondary structure assignments.
• Structural Biology Research: Enables investigation of protein dynamics and interactions via contact maps and Ramachandran plots.
• Teaching Structural Biology: Provides secondary structure assignments and plots for instructional and educational use in structural biology.

Methodology:

STRIDE applies a knowledge-based algorithm that integrates hydrogen-bond energy calculations with statistical models of backbone torsional angles.