ProDy

ProDy provides comprehensive analysis of protein structural dynamics by quantifying conformational variation and relating experimental structures to theoretical equilibrium motions.

Key Features:

• Structure-Based Analysis: Quantitative characterization of structural variations within heterogeneous datasets of experimentally resolved structures, including families, subfamilies, mutants, sequence homologues, and complexes with substrates, ligands, or inhibitors.
• Comparative Dynamics: Comparison of observed structural variation with theoretically predicted equilibrium dynamics to assess correspondence between experimental and theoretical motions.
• Enhanced Interfacing and Parsing: Improved interfacing with databases and parsing of additional file formats for handling diverse structural datasets.
• Signature Dynamics (SignDy): Analysis of family-specific signature dynamics to identify conformational patterns characteristic of protein families.
• Cryo-Electron Microscopy Integration (CryoDy): Collective dynamics analysis of supramolecular systems using cryo-EM density maps.
• Essential Site Scanning: Identification of sites that modulate global protein dynamics to pinpoint residues critical for functional motion.
• Visualization Tools: Helper functions for visualizing principal conformational changes across different functional states.
• Extensible API: An application programming interface for extending the software and implementing new computational methods.

Scientific Applications:

• Protein dynamics characterization: Quantifying conformational variability within protein families, mutants, homologues, and complexes.
• Mechanistic interpretation: Relating equilibrium dynamics to observed structural changes to interpret mechanisms of conformational transitions.
• Target site identification: Locating essential sites that influence global dynamics for functional studies and modulation.
• Supramolecular assembly analysis: Studying collective motions of large biomolecular assemblies using cryo-EM density maps.
• Drug design support: Informing inhibitor and modulator design through dynamic structural information.

Methodology:

ProDy applies computational analysis that leverages experimentally resolved structural datasets and theoretical equilibrium dynamics, and supports integration of additional methods and file formats.