Chromatin Dynamics

Chromatin Dynamics analyzes nucleic acid flexibility and chromatin interactions using multiscale computational models to characterize structure, dynamics, and energetics.

Key Features:

• Structure Incorporation and Optimization: Incorporates nucleic acid structures from Protein Data Banks (PDB) and fills structural gaps and resolves inconsistencies to produce complete models.
• Canonical Structure Definition: Supports definition of canonical nucleic acid structures using predefined internal libraries, including average and sequence-adapted models.
• Custom Conformation Creation: Generates specific nucleic acid conformations directly from sequences.
• Flexibility Exploration Methods: Implements Colorless Wormlike-Chain Model, base-pair resolution mesoscopic model, and atomistic molecular dynamics simulations using various protocols and force fields.
• Trajectory Visualization and Analysis: Provides trajectory visualization and analytical tools including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness evaluation, energy decomposition, principal components analysis, and in silico NMR spectra generation.

Scientific Applications:

• Chromatin structural analysis: Characterizes chromatin and nucleic acid structural properties at multiple scales.
• Nucleic acid flexibility studies: Quantifies flexibility and mechanical properties of nucleic acids using coarse-grained and atomistic models.
• Nucleic acid–protein interaction analysis: Analyzes dynamics and energetics relevant to nucleic acid–protein complexes.
• Gene regulation and epigenetics studies: Supports investigation of structural mechanisms underlying gene regulation and epigenetic processes.

Methodology:

Combines theoretical models and computational simulations using coarse-grained approaches (Colorless Wormlike-Chain and base-pair resolution mesoscopic models) and atomistic molecular dynamics with various protocols and force fields, coupled to analyses such as Cartesian analysis, essential dynamics, principal components analysis, helical analysis, stiffness evaluation, energy decomposition, and in silico NMR spectra generation.