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

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

Software for predicting translation initiation rates in bacteria

Script to facilitate the making of horizontal scripts

Python implementation of Nussinov RNA folding algorithm and recursive backtrack.

[NeurIPS 2024] A Multi-task Benchmark Dataset for Nanopore Sequencing.

Multiscale dataset of non-coding RNA structures, including sequences, secondary structures, non-canonical interactions, 3D geometrical descriptors, and sequence homology.

[ICPR 2024] Knowledge from Large-Scale Protein Contact Prediction Models can be Transferred to the Data-Scarce RNA Contact Prediction Task

This is the official codebase for RESM: Capturing sequence and structure encoding of RNAs by mapped transfer learning from ESM (evolutionary scale modeling) protein language model

RNA/DNA 3D structure alignment tool

Library for processing RNA structures using PDB, DSSR and other data

Construct atomistic (AA) model from Three-Interaction-Site (TIS) coarse-grained model of RNA/DNA

Bialignment of RNAs and proteins

sticky finder for "sticky" RNA sequence identification

Solving RNA Folding Problems with Linear/Integer Programming

A quantum algorithm (Quantum Annealing Based) for prediciting RNA secondary structure for small sequences like those of miRNA. This was compared with the classical algorithm ViennaRNA

Adaptation of RNAdegformer and RiNALMo to predict RNA degradation likelihood

extremely simple UFold demo

Architecture of Large Projects in Bioinformatics (University project)