Toyfold 3

Calculations of RNA tertiary structure ensembles and free energies in 3D

Author: Rhiju Das, 2020

Goals

• Actual predictions for C_eff and structural ensembles for circular RNA
• Explore sampling of ribose rings as a 'sub problem' in atomic reconstruction.
• Actual predictions for nearest neighbor energies
• Structural ensembles for helices
• Test factorization of free energy in terms of local motif energy (including K_d); motif modularity costs; tertiary closure.
• Test simple analytic representations of translation/rotation SE(3) distributions in tertiary closure costs, including Gaussian models and harmonic transforms.
• Rapid simulations to test partitition function calcs -- including tertiary structure -- in MATLAB ('build a fold').

Notes

• Intended to be a port of ToyFold 2D to the 'real world', RNA folding in three dimensions
• Manipulation of SE(3) transforms for RNA inspired by loop_close repo (and 6D loop_close implementation in Rosetta).
• Starting with backbone conformational preferences drawn from ribosomal 23S RNA (4YBB).

Getting Started

• Add to your paths: scripts/ and subdirectories.
• Check notes/ for TextEdit viewable notes on current modeling status
• Check runs/ for example commands. First load data saved via load 01_circularBB_test.mat. Then check the commands in, say, 01_circularBB_test.m, particularly the code block at the end that runs sample_circle_trajectory.