emDNA

emDNA minimizes the energy of DNA and DNA–protein complexes to model mesoscale structural responses and relate DNA structure to function.

Key Features:

• Implementation: Implemented in C++.
• Base-pair step modeling: Models nucleic acids at the base-pair step level using rigid-body parameters.
• Energy minimization: Performs energy minimization of DNA and DNA–protein complexes.
• Opened and closed fragments: Simulates both opened and closed DNA fragments.
• Geometrical constraints: Enforces geometric constraints including fixed end-to-end distances and rotations.
• Elastic models: Integrates built-in or user-provided elastic models for sequence-specific mechanical properties.
• Fixed base-pair positioning: Allows fixing the orientation and position of specified base pairs to represent protein-bound or melted DNA.
• Large-scale models: Can construct and optimize models extending to hundreds of base pairs.
• Sequence-specific inputs: Builds models from local, sequence-specific features derived from experimental data.
• Mesoscale bridging: Bridges all-atom molecular dynamics studies and coarse-grained simulations to study mesoscale behavior.

Scientific Applications:

• Structure–function analysis: Elucidating relationships between DNA structure and biological function.
• Protein–DNA interaction modeling: Simulating the structural effects of protein-bound DNA regions.
• Mesoscale organization studies: Investigating mesoscale organization of DNA, including loops and minicircles.
• Integration of experimental configurations: Incorporating experiment-specific configurations into higher-order 3D models.
• Thermal equilibrium optimization: Optimizing DNA structures at thermal equilibrium to assess mechanical responses.

Methodology:

Computational steps explicitly include modeling at the base-pair step level with rigid-body parameters and performing energy minimization using built-in or user-provided elastic models, while enforcing specified geometrical constraints and fixed base-pair orientations/positions to optimize structures at thermal equilibrium.