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

Repo for the comradesOO R package. Designed for the analysis of RNA structural data obtained through RNA cross-linking and high-throughput sequencing experiments

locality-aware invariant Point Attention-based RNA ScorEr

RiboNucleic Acid (RNA) Language Model

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

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

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

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

nucleic acid folding

Alignment of RNAs

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.

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

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

Maven project for the bioinformatic application LoopMatcher (aka LASLO).

Visualizes the secondary structure of RNA using Verna

Julia interface to ViennaRNA for RNA structure prediction and analysis

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

RNA folding and codon optimization in pure Rust

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