Resources

Here's a list of various resources, documents and force-field parameters. If you find this useful for your work, a citation would be very much appreciated :)

SOFTWARE

baRNAba: a tool for analyzing RNA three-dimensional structures. Find RNA three dimensional motifs, cluster 3D structures. calculate distances. Back-calculate NMR parameters from structure and much more.

FORCE-FIELD PARAMETERS

EEF1-SB parameters. Parameters for the implicit solvent model for protein simulations.
AMBER99SB + Parmbsc0 + Chi_ol force-field parameters for GROMACS.

MD TRAJECTORIES and DATABASES

Temperature replica-exchange on RNA tetranucleotides
Well-tempered metadynamics simulations on RNA tetraloops
Cluster analysis of RNA tetraloops

DOCUMENTS

Short notes on back-calculations of 3J scalar couplings using Karplus relationships in RNA

VIDEOS

Animations of the folding pathways of RNA tetraloops obtained with our stop-motion approach