rna-structure

gRNAde is a Generative AI framework for inverse design of 3D RNA structure and function

Trainable PyTorch framework for developing protein, RNA and complex models.

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...

RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

Analyse Nucleic Acids Structure and Simulations with baRNAba

A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.

Software for predicting translation initiation rates in bacteria

CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

A platform to do RNA science

TISIGNER: Unleash the power of synthetic biology

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

RNA secondary structure prediction tool

Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.

Script to facilitate the making of horizontal scripts

RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io

pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.

CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data

Transformer + GAT for RNA chemical reactivity prediction| Stanford Ribonanza

Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/archive/master.zip