GitHub topics: rna-structure-prediction

Repositories

lbcb-sci/RiNALMo

RiboNucleic Acid (RNA) Language Model

Language: Python - Size: 279 KB - Last synced at: 10 days ago - Pushed at: 11 days ago - Stars: 105 - Forks: 20

TheCOBRALab/HFold

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

Language: C++ - Size: 20.8 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 4

syseitz/RNAtedistance

Calculating Tree Edit Distance for RNA Structures in Dot Bracket Notation

Language: C - Size: 546 KB - Last synced at: 24 days ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

PaddlePaddle/PaddleHelix

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

Language: Python - Size: 131 MB - Last synced at: 23 days ago - Pushed at: 7 months ago - Stars: 1,064 - Forks: 229

febos/SQUARNA

RNA secondary structure prediction tool

Language: Jupyter Notebook - Size: 162 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 16 - Forks: 2

febos/SQUARNA-data

SQUARNA benchmark data

Language: Jupyter Notebook - Size: 105 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

RosettaCommons/PyRosetta.notebooks

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

Language: Jupyter Notebook - Size: 353 MB - Last synced at: 22 days ago - Pushed at: 10 months ago - Stars: 568 - Forks: 160

JLP-BioInf/rnaCrosslinkOO

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

Language: R - Size: 4.73 MB - Last synced at: 11 days ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

TheCOBRALab/CCJ

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

Language: C++ - Size: 1.75 MB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 1

TheCOBRALab/DinoKnot

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

Language: C++ - Size: 13 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 4

TheCOBRALab/Iterative-HFold

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

Language: C++ - Size: 5.71 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 3 - Forks: 5

marcom/ViennaRNA.jl

Julia interface to ViennaRNA for RNA structure prediction and analysis

Language: Julia - Size: 328 KB - Last synced at: 2 months ago - Pushed at: about 1 year ago - Stars: 22 - Forks: 1

XieResearchGroup/Physics-aware-Multiplex-GNN

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

Language: Python - Size: 1.43 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 54 - Forks: 10

s-will/LocARNA

Alignment of RNAs

Language: C++ - Size: 20.8 MB - Last synced at: 2 months ago - Pushed at: 11 months ago - Stars: 24 - Forks: 4

Bhattacharya-Lab/lociPARSE

locality-aware invariant Point Attention-based RNA ScorEr

Language: Python - Size: 26.6 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 5 - Forks: 0

Lattice-Automation/seqfold

nucleic acid folding

Language: Python - Size: 136 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 79 - Forks: 12

yikunpku/RNA-MSM

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.

Language: Python - Size: 13.2 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 38 - Forks: 4

csfoo/contrafold-se

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

Language: C++ - Size: 168 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 8 - Forks: 4

Neo-Panther/RNA-Secondary-Visualizer

Visualizes the secondary structure of RNA using Verna

Language: C - Size: 1.77 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

marcom/LinearFold.jl

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

Language: Julia - Size: 36.1 KB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

dmancilla85/java-mvn-laslo

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

Language: Java - Size: 8.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

gtDMMB/GTFoldPython

Python bindings to use the historical GTFold library natively in the RNADB construction script and natively with Python3. See the WIKI pages for documentation and installation notes.

Language: C - Size: 16 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

abondrn/polymerust

RNA folding and codon optimization in pure Rust

Language: Rust - Size: 116 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Urinx/RNAWorld

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

Language: Python - Size: 1.19 MB - Last synced at: 2 months ago - Pushed at: almost 6 years ago - Stars: 12 - Forks: 0

mmagnus/EvoClustRNA

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

Language: Jupyter Notebook - Size: 164 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 5

rooselvelt6/UCISAHUAPA Fork of odoo/odoo

Agente Inteligente Basado en Redes Neuronales Artificiales para la Identificación de los determinantes de la estadía de los pacientes de la UCI del HUAPA de Cumaná, estado Sucre

Language: Python - Size: 2.01 GB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 1 - Forks: 0

rna-structure-prediction 34 rna 16 rna-structure 12 rna-folding 10 bioinformatics 6 pseudoknot-structures 4 rna-secondary-structure-prediction 3 machine-learning 3 structure-prediction 3 biology 3 hfold 3 structural-biology 3 secondary-structure 3 bioinformatics-tool 3 alignment 3 rna-secondary-structure 3 biological-data-analysis 2 prediction 2 prediction-algorithm 2 pseudoknot 2 2d 2 secondary-structure-prediction 2 single-sequence 2 structure 2 dna 2 rosetta 2 python3 2 julia 2 deep-learning 2 protein-structure-prediction 2 protein-folding 2 protein-docking 2 protein-design 2 rna-structural-analysis 2 language-model 2 apache2 1 health 1 hospital 1 investigation 1 keras-models 1 keras-neural-networks 1 keras-ten 1 linux-server 1 odoo11 1 patient-data 1 tensorflow 1 simrna 1 farna 1 farfar 1 reinforcement-learning 1 gym-environment 1 codon-optimization 1 rna-seq-analysis 1 monte-carlo-simulation 1 python-library 1 python-bindings 1 hfold-iterative 1 blast 1 blast-search 1 distance-matrix 1 distance-matrix-computation 1 nussinov 1 nussinov-algorithm 1 population-determination 1 population-genetics 1 population-genomics 1 rna-design 1 nim 1 bindings 1 vcf-file-distance-matrix 1 rna-puzzle 1 rna3d 1 rna-pdb 1 pdb-files 1 pdb 1 xml 1 virtualenv 1 uci 1 ubuntu1804 1 vcf-files 1 interacting-hfold 1 hfold-interacting 1 ccj 1 rna-crosslinking 1 r 1 psoralen 1 comrades 1 pyrosetta 1 jupyter-notebook 1 google-colab 1 self-supervised-learning 1 representation-learning 1 ppi 1 molecule-design 1 graph-networks 1 dti 1 deeplearning 1 ddi 1 biocomputing 1 splice-site-prediction 1