rna-structure-prediction

There are 3 repositories under rna-structure-prediction topic.

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
biocomputing ddi deeplearning dti graph-networks machine-learning molecule-design ppi protein-design protein-docking protein-folding protein-structure-prediction representation-learning rna-structure-prediction self-supervised-learning
Language:Python 1022
RosettaCommons / PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
dna google-colab jupyter-notebook protein-design protein-docking protein-folding protein-structure-prediction pyrosetta rna-structure-prediction rosetta
Language:Jupyter Notebook 506
Lattice-Automation / seqfold
nucleic acid folding
dna dna-folding dna-structure-prediction folding rna rna-folding rna-structure-prediction structure-prediction
Language:Python 86
lbcb-sci / RiNALMo
RiboNucleic Acid (RNA) Language Model
bioinformatics biology foundation-model language-model rna rna-secondary-structure rna-seq rna-structure-prediction secondary-structure splice-site-prediction structural-biology
Language:Python 76
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"
computational-biology computational-chemistry docking geometric-deep-learning graph-neural-networks machine-learning protein-ligand-interactions rna-structure-prediction
Language:Python 57
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.
bioinformatics language-model rna rna-structure-prediction
Language:Python 54
s-will / LocARNA
Alignment of RNAs
alignment rna-structure-prediction rna-structural-analysis
Language:C++ 24
mjendrusch / nimna
DNA/RNA folding in Nim
bioinformatics rna-structure-prediction nim bindings rna-design
Language:Nim 22
marcom / ViennaRNA.jl
Julia interface to ViennaRNA for RNA structure prediction and analysis
rna rna-folding rna-structure-prediction julia rna-secondary-structure-prediction
Language:Julia 21
mmagnus / emacs-pdb-mode
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.
pdb-files pdb rna-structure-prediction rna-structure rna-pdb
Language:Emacs Lisp 14
mmagnus / EvoClustRNA
RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io
rna rna-structure rna-structure-prediction simrna rosetta farna farfar
Language:Jupyter Notebook 14
Urinx / RNAWorld
A gym environment for the research which apply the reinforcement learning algorithm to the RNA structure prediction
gym-environment reinforcement-learning rna-structure-prediction
Language:Python 12
csfoo / contrafold-se
CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data
rna-structure-prediction rna-structure conditional-random-fields machine-learning bioinformatics-algorithms
Language:C++ 9
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
rna-puzzle rna-structure rna-structure-prediction
Language:Shell 9
Bhattacharya-Lab / lociPARSE
locality-aware invariant Point Attention-based RNA ScorEr
attention-network deep-learning rna-scoring rna-structure-prediction
Language:Python 6
marcom / LinearFold.jl
Julia interface to LinearFold RNA structure prediction programs: LinearFold, LinearPartition, LinearSampling, and LinearTurboFold
julia rna rna-folding rna-structure-prediction
Language:Julia 6
HosnaJabbari / Iterative-HFold
RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding
hfold hfold-iterative iterative-hfold pseudoknot-structures rna rna-folding rna-structure rna-structure-prediction
Language:C++ 3
HosnaJabbari / CCJ
MFE method for predicting the psuedoknotted secondary structures of RNA sequences.
rna-structure-prediction rna-folding rna rna-structure ccj pseudoknot-structures
Language:C++ 2
HosnaJabbari / DinoKnot
RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding
hfold hfold-interacting interacting-hfold pseudoknot-structures rna rna-folding rna-structure rna-structure-prediction
Language:C++ 2
rooselvelt6 / UCISAHUAPA
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
health odoo11 xml python3 tensorflow rna-structure-prediction deep-learning investigation uci hospital patient-data apache2 linux-server keras-neural-networks keras-ten keras-models virtualenv ubuntu1804
Language:Python 2
cas-bioinf / rboAnalyzer
Tool for analysing BLAST output for ncRNA sequences
blast blast-search rna rna-structure-prediction
Language:Python 1
ChevronOne / Tools-For-Computational-Biology
Tools For Computational Biology
distance-matrix distance-matrix-computation vcf-files rna-structure-prediction rna-folding vcf-file-distance-matrix nussinov-algorithm nussinov population-determination population-genetics population-genomics
Language:C++ 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.
python3 rna-seq-analysis rna-structure-prediction python-bindings python python-library
Language:C 1
gtDMMB / RNAprofilingV2
rna rna-structure-prediction
Language:Python 1
HosnaJabbari / HFold
RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding
hfold pseudoknot-structures rna rna-folding rna-structure rna-structure-prediction
Language:C 1
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
comrades psoralen r rna-crosslinking rna-structure rna-structure-prediction
Language:R 1
Neo-Panther / RNA-Secondary-Visualizer
Visualizes the secondary structure of RNA using Verna
c rna-structure-prediction svg visualization doxygen-documentation html-css
Language:C 1
abondrn / polymerust
RNA folding and codon optimization in pure Rust
bioinformatics codon-optimization rna-structure-prediction
Language:Rust 0
dmancilla85 / java-mvn-laslo
Maven project for the bioinformatic application LoopMatcher (aka LASLO).
java biojava maven bioinformatics-tool rnafold rna-structure-prediction
Language:Java 0
juvion / EBMonteCarlo
monte-carlo-simulation rna-structure-prediction rna-folding
Language:C++

rna-structure-prediction

PaddlePaddle / PaddleHelix

RosettaCommons / PyRosetta.notebooks

Lattice-Automation / seqfold

lbcb-sci / RiNALMo

XieResearchGroup / Physics-aware-Multiplex-GNN

yikunpku / RNA-MSM

s-will / LocARNA

mjendrusch / nimna

marcom / ViennaRNA.jl

mmagnus / emacs-pdb-mode

mmagnus / EvoClustRNA

Urinx / RNAWorld

csfoo / contrafold-se

mmagnus / RNA-Puzzles-Standardized-Submissions

Bhattacharya-Lab / lociPARSE

marcom / LinearFold.jl

HosnaJabbari / Iterative-HFold

HosnaJabbari / CCJ

HosnaJabbari / DinoKnot

rooselvelt6 / UCISAHUAPA

cas-bioinf / rboAnalyzer

ChevronOne / Tools-For-Computational-Biology

gtDMMB / GTFoldPython

gtDMMB / RNAprofilingV2

HosnaJabbari / HFold

JLP-BioInf / rnaCrosslinkOO

Neo-Panther / RNA-Secondary-Visualizer

abondrn / polymerust

dmancilla85 / java-mvn-laslo

juvion / EBMonteCarlo