SRide

SRide identifies stabilizing residues (SRs) in proteins from known three-dimensional structures to characterize determinants of protein stability, originally developed for TIM-barrel proteins and generalized to all proteins with solved structures.

Key Features:

• Residue Selection Criteria: Residues are evaluated using surrounding hydrophobicity, long-range order, evolutionary conservation score, and membership in stabilization centers.
• Surrounding Hydrophobicity: Assesses hydrophobic interactions within a residue's spatial neighborhood relevant to protein stability.
• Long-Range Order: Evaluates the order and organization of residues over long distances within the three-dimensional structure.
• Conservation Score: Incorporates evolutionary conservation to prioritize residues with likely functional or structural importance.
• Stabilization Centers: Requires residues to be part of stabilization centers to qualify as stabilizing residues.
• Spatial Interaction Focus: Integrates methods that analyze spatial interactions among residues rather than sequential contacts.
• Parameter Definitions and Thresholds: Employs established definitions and thresholds for each parameter to determine SRs.

Scientific Applications:

• Protein Engineering: Pinpoints stabilizing residues to guide design and modification of proteins for enhanced stability or altered properties.
• Homology Modeling: Provides stability-related insights that inform and improve homology model predictions.
• Understanding Protein Folds: Helps elucidate the structural reasons behind the stability of specific protein folds.

Methodology:

The algorithm integrates multiple methods that analyze spatial residue interactions rather than sequential ones and applies defined parameter definitions and thresholds for surrounding hydrophobicity, long-range order, conservation score, and stabilization-center membership.