rna-structure-prediction | Topic

Topic: "rna-structure-prediction"

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: 133 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1,078 - Forks: 229

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: 2 months ago - Pushed at: 12 months ago - Stars: 568 - Forks: 160

lbcb-sci/RiNALMo

RiboNucleic Acid (RNA) Language Model

Language: Python - Size: 279 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 105 - Forks: 20

Lattice-Automation/seqfold

nucleic acid folding

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

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: 9 months ago - Pushed at: 9 months ago - Stars: 54 - Forks: 10

RFOLD/RhoFold

Open source code for RhoFold: Fast and Accurate RNA 3D Structure Prediction with Deep Learning.

Language: Python - Size: 30.8 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 39 - Forks: 6

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: about 1 year ago - Pushed at: about 1 year ago - Stars: 38 - Forks: 4

s-will/LocARNA

Alignment of RNAs

Language: C++ - Size: 20.8 MB - Last synced at: 4 months ago - Pushed at: 12 months ago - Stars: 24 - Forks: 4

marcom/ViennaRNA.jl

Julia interface to ViennaRNA for RNA structure prediction and analysis

Language: Julia - Size: 328 KB - Last synced at: 4 months ago - Pushed at: over 1 year ago - Stars: 22 - Forks: 1

mjendrusch/nimna

DNA/RNA folding in Nim

Language: Nim - Size: 861 KB - Last synced at: 7 days ago - Pushed at: over 7 years ago - Stars: 21 - Forks: 0

febos/SQUARNA

RNA secondary structure prediction tool

Language: Jupyter Notebook - Size: 162 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 18 - Forks: 2

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

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.

Language: Emacs Lisp - Size: 351 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 13 - Forks: 6

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: 4 months ago - Pushed at: almost 6 years ago - Stars: 12 - Forks: 0

mmagnus/RNA-Puzzles-Standardized-Submissions

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

Language: Shell - Size: 104 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 7

csfoo/contrafold-se

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

Language: C++ - Size: 168 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 4

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: 3 months ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0

Bhattacharya-Lab/lociPARSE

locality-aware invariant Point Attention-based RNA ScorEr

Language: Python - Size: 26.6 MB - Last synced at: 9 months ago - Pushed at: 10 months ago - Stars: 5 - Forks: 0

TheCOBRALab/Iterative-HFold

RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

Language: C++ - Size: 5.71 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 5

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: 8 days ago - Pushed at: 8 days ago - Stars: 2 - Forks: 0

TheCOBRALab/CCJ

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

Language: C++ - Size: 1.43 MB - Last synced at: 23 days ago - Pushed at: 4 months ago - Stars: 2 - Forks: 2

TheCOBRALab/DinoKnot

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

Language: C++ - Size: 13 MB - Last synced at: 4 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 4

TheCOBRALab/HFold

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

Language: C++ - Size: 20.8 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1 - 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: over 1 year ago - Stars: 1 - Forks: 0

gtDMMB/RNAprofilingV2

Language: Python - Size: 570 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

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: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

cas-bioinf/rboAnalyzer

Tool for analysing BLAST output for ncRNA sequences

Language: Python - Size: 4.82 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 2

ChevronOne/Tools-For-Computational-Biology

Tools For Computational Biology

Language: C++ - Size: 2.81 MB - Last synced at: over 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 1

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: almost 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0