RNA-FRETools/fretlabel: Release v0.2.0

FRETlabel is a PyMOL plugin to label nucleic acids with explicit fluorescent dyes. It aims to facilitate the workflow of setting up, running and evaluating molecular dynamics simulations with explicit organic fluorophores for in silico FRET calculations.

Specifically, FRETlabel includes the following features:

• PyMOL plugin for fluorescent labeling: Label your nucleic acid of interest with the click of a button. The PyMOL plugin extends the AMBERDYES package (Graen et al. JCTC 2014) geometries and force field parameters of common nucleic acid linker chemistries.
• Build new fragments interactively: Tutorials guide you step-by-step through the process of creating new base, linker and dye fragments by integrating with established pipelines for topology generation such as Antechamber and Acpype.
• FRET prediction: Calculate FRET distributions from MD simulation with all-atom organic dyes. FRETlabel integrates with FRETraj to compute photon bursts based on distance R_DA(t) and orientation trajectories κ²(t) of the fluorophores.