CGeNArateWeb

CGeNArateWeb simulates the structure and dynamics of chromatin fibers using a coarse-grained Hamiltonian, enabling dynamic representations of linear, circular, and protein-DNA segments at kilobase-range scales.

Key Features:

• Coarse-grained simulation: Employs a Langevin dynamics coarse-grained model with a machine-learning fitted C1'-resolution Hamiltonian to simulate naked DNA and protein-bound chromatin fibers.
• Atomistic back-mapping: Converts coarse-grained trajectories to atomistic resolution using a machine-learning algorithm trained on a large database of molecular dynamics simulations.
• Nucleic acid-specific analysis: Provides an extensive set of nucleic acid-specific analysis tools for trajectory analysis.
• Flexible input options: Supports simulation of linear DNA, circular DNA, and protein-DNA segments.

Scientific Applications:

• Chromatin fiber modeling: Generates structural and dynamic models of large protein-bound and free DNA segments, transforming conceptual cartoons into structural and dynamical models.
• DNA structure and dynamics analysis: Enables study of three-dimensional organization and dynamic behavior of naked DNA and protein-bound chromatin fibers at kilobase-range scales.

Methodology:

CGeNArateWeb uses a Langevin dynamics coarse-grained model with a machine-learning fitted C1'-resolution Hamiltonian. Coarse-grained trajectories are back-mapped to atomistic resolution using a machine-learning algorithm trained on a large database of molecular dynamics simulations.