cgNA+web

cgNA+web visualizes sequence-dependent ground states of double-stranded nucleic acids using the cgNA+ coarse-grain model to characterize equilibrium statistical-mechanics effects on shape and stiffness.

Key Features:

• Sequence-Dependent Visualization: Visualizes ground states of dsNA fragments with arbitrary sequences and highlights how sequence-dependent perturbations alter shape and stiffness away from an idealized double-helical structure.
• cgNA+ coarse-grain model: Implements the cgNA+ coarse-grain model to capture sequence-dependent perturbations and fluctuations and to predict equilibrium ground-state shapes.
• Modeling Versatility: Supports parameter sets for double-stranded DNA (dsDNA), including sequences with epigenetically modified CpG dinucleotide steps, double-stranded RNA (dsRNA), and DNA:RNA hybrid double-helical fragments.
• Comparative Analysis: Enables comparison of ground-state shapes between different sequences of the same dsNA or analogous sequences across different dsNA types.

Scientific Applications:

• Mechanical Property Analysis: Analyzing how specific sequences influence the mechanical properties and stability (shape and stiffness) of dsNAs.
• Epigenetic Modification Effects: Investigating the structural and mechanical impacts of epigenetically modified CpG dinucleotide steps in DNA.
• RNA and Hybrid Structure Analysis: Exploring sequence-dependent structural variations of dsRNA and DNA:RNA hybrid fragments.

Methodology:

The cgNA+ coarse-grain model captures sequence-dependent perturbations and fluctuations, accounts for deviations from an idealized double-helical structure, and predicts equilibrium ground-state shapes of dsNAs.