NAFlex

NAFlex analyzes nucleic acid flexibility at multiple scales to characterize dynamic properties of isolated or molecule-bound DNA and RNA.

Key Features:

• Structure Integration and Refinement: Incorporates nucleic acid structures from the Protein Data Bank (PDB) and completes structural gaps and resolves inconsistencies to ensure high-quality input models.
• Canonical Structure Definition: Defines canonical nucleic acid structures using predefined internal libraries, including average and sequence-adapted conformations.
• Custom Conformation Creation: Generates specific nucleic acid conformations directly from nucleotide sequences.
• Flexibility Exploration Methods: Implements a Colorless Wormlike-Chain model, a base-pair-resolution mesoscopic model, and atomistic molecular dynamics simulations with support for multiple protocols and force fields.
• Trajectory Analysis Tools: Provides visualization and analysis of simulation or imported trajectories, including Cartesian analysis, essential dynamics, helical analysis, local and global stiffness assessments, energy decomposition, principal components analysis, and in silico NMR spectra generation.

Scientific Applications:

• Structural Biology: Characterizes conformational changes and dynamic behavior of DNA and RNA in isolated or complexed states.
• Drug Design: Analyzes how small molecules or proteins interact with nucleic acids considering flexibility and conformational ensembles.
• Genomics and Epigenetics: Investigates sequence-specific structural adaptations and their potential influence on gene regulation.

Methodology:

Refines PDB-derived structures and applies multi-scale computational modeling including Colorless Wormlike-Chain and base-pair-resolution mesoscopic models, atomistic molecular dynamics simulations with various protocols and force fields, and trajectory analyses such as Cartesian analysis, essential dynamics, helical analysis, stiffness assessments, energy decomposition, principal components analysis, and in silico NMR spectra generation.