Repositories list

• spqr

  Public
  Simulation code for the prediction of RNA structures.

  C

  •

  GNU General Public License v3.0

  •3•10•0•0•Updated Jan 13, 2025Jan 13, 2025

• barnaba

  Public
  Analyse Nucleic Acids Structure and Simulations with baRNAba

  modelingmolecular-dynamicsrna-structure+ 3rnarna-foldingpython

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •15•41•14•3•Updated Mar 20, 2024Mar 20, 2024

• ff

  Public
  Force Fields

  Shell

  •8•13•0•0•Updated Oct 25, 2022Oct 25, 2022

• tetraloops-trajectories

  Public
  0•1•2•0•Updated Apr 3, 2022Apr 3, 2022

• shape-md

  Public
  0•0•0•0•Updated Apr 3, 2022Apr 3, 2022

• rna-enhanced-sampling

  Public
  TeX

  •1•0•0•0•Updated Dec 20, 2017Dec 20, 2017

• oligonucleotides-kinetics

  Public
  IPython analysis notebooks for Markov state models of oligonucletides

  Jupyter Notebook

  •1•5•1•0•Updated Aug 28, 2017Aug 28, 2017

• plumed2

  Public
  Public branches developed in our group

  296•0•0•0•Updated Jun 6, 2017Jun 6, 2017

• dftb-pucker-corrections

  Public
  Corrections for RNA pucker using DFTB

  Shell

  •0•1•0•0•Updated Jul 26, 2016Jul 26, 2016

• 4nt-trajectories

  Public
  Trajectories of tetranucleotides

  Shell

  •1•0•0•0•Updated Jul 11, 2016Jul 11, 2016

• demux

  Public
  Perl script to demux gromacs trajectories, with a fix that allows long trajectories to be processed correctly

  Perl

  •1•6•0•0•Updated Mar 24, 2016Mar 24, 2016

• smd-reweight

  Public
  C++

  •1•1•0•0•Updated Apr 8, 2015Apr 8, 2015