nucleic acid folding

Analyse Nucleic Acids Structure and Simulations with baRNAba

A lua package for designing DNA.

Julia interface to ViennaRNA for RNA structure prediction and analysis

Julia interface to the RNAstructure program suite for RNA structure prediction and analysis

Python implementation of Nussinov RNA folding algorithm and recursive backtrack.

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

RNA design tool that utilizes reinforcement learning

Nucleic acid secondary structure prediction and analysis

Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model

RAFFT: RNA structure and folding dynamics predictions using the fast Fourier transform

A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

🧬 Zuker: An RNA secondary structure prediction algorithm

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

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

Faster algorithms for RNA-folding using the Four-Russians method

This repository contains a comprehensive solution for the Stanford RNA 3D Folding Kaggle competition, implementing advanced machine learning techniques for predicting RNA 3D structures from sequence data. The project demonstrates expertise in bioinformatics, deep learning, and scientific computing.

Tools For Computational Biology

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding