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

nucleic acid folding

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

RiboNucleic Acid (RNA) Language Model

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.

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

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

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

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

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.

Alignment of RNAs

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

Tool for analysing BLAST output for ncRNA sequences

MFE method for predicting the psuedoknotted secondary structures of RNA sequences.

Tools For Computational Biology

Julia interface to ViennaRNA for RNA structure prediction and analysis

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