Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

RiboNucleic Acid (RNA) Language Model

nucleic acid folding

Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"

Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.

structRFM: A fully open structure-guided RNA foundation model for robust structural and functional inference

Alignment of RNAs

Julia interface to ViennaRNA for RNA structure prediction and analysis

DNA/RNA folding in Nim

RNA secondary structure prediction tool

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.

A gym environment for the research which apply the reinforcement learning algorithm to the RNA structure prediction

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

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

Julia interface to LinearFold RNA structure prediction programs: LinearFold, LinearPartition, LinearSampling, and LinearTurboFold

locality-aware invariant Point Attention-based RNA ScorEr

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding