STRIDER

STRIDER estimates inter- and intra-molecular steric hindrance in biomacromolecules by calculating atomic overlaps using van der Waals radii of 117 elements to inform modeling and analysis of carbohydrates, lipids, nucleic acids, proteins, and their complexes with small molecules.

Key Features:

• Steric Hindrance Estimation: Calculates inter- and intra-molecular steric hindrances using van der Waals radii of 117 elements.
• Metal Coordination Analysis: Identifies and reports the coordination number of 64 metals and their interaction patterns.
• Conformer Ensemble Analysis: Analyzes multiple conformers to address sampling issues inherent in flexible docking and to assess conformational variability.
• Input Format Support: Accepts Cartesian coordinates provided in Protein Data Bank (PDB) format as molecular input.
• PyMOL Session Export: Generates a PyMOL session file for offline visualization of steric hindrance results.

Scientific Applications:

• Computational Structure Validation: Validates biomacromolecular models by identifying steric clashes and structural constraints.
• De novo Design and Docking: Informs de novo design and flexible docking by assessing steric compatibility between partners.
• Complement to Experimental Methods: Provides structural insight that complements cryo-electron microscopy-derived models through steric analysis.
• Conformational Dynamics and Virtual Screening: Supports exploration of conformational ensembles and aids structure-based virtual screening by evaluating steric feasibility.

Methodology:

Analyzes the spatial arrangement of atoms from Cartesian PDB coordinates, uses van der Waals radii of 117 elements to estimate steric clashes, identifies coordination numbers and interaction patterns for 64 metals, analyzes multiple conformers to address sampling in flexible docking, and exports results as a PyMOL session file.