cgHeliParm

cgHeliParm computes helical parameters from Martini-based coarse-grained double-stranded DNA molecular dynamics trajectories to enable conformational analysis at the coarse-grained level.

Key Features:

• Helical Parameter Calculation: Computes base, base pair, and base pair step helical parameters for coarse-grained DNA.
• Martini Trajectory Compatibility: Analyzes Martini coarse-grained molecular dynamics trajectories directly without requiring conversion to atomistic models.
• Implementation: Implemented as Python-based software for computational analysis.
• Reference Files: Uses base reference files such as CG_X_std.lib for parameter calculations.
• Downstream Analysis: Includes R scripts for further data analysis and visualization of results.

Scientific Applications:

• Conformational Analysis: Enables conformational studies of double-stranded DNA in Martini coarse-grained molecular dynamics simulations.
• Structural Dynamics: Supports investigation of large-scale structural dynamics of DNA without atomistic detail.
• Biomolecular Interaction Studies: Facilitates analysis of DNA interactions within complex biomolecular systems using coarse-grained models.

Methodology:

Python code reads Martini coarse-grained MD trajectories, computes base, base pair, and base pair step helical parameters using reference files such as CG_X_std.lib, and provides R scripts for downstream analysis and visualization.