rna-structure

There are 3 repositories under rna-structure topic.

OpenComplex
baaihealth / OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
alphafold2 protein-structure pytorch rna-structure
Language:Python 258
chaitjo / geometric-rna-design
gRNAde: Geometric Deep Learning for 3D RNA inverse design (ICLR 2025 Spotlight)
biomolecule-design geometric-deep-learning graph-neural-networks inverse-design pytorch pytorch-geometric rna-structure
Language:Jupyter Notebook 220
rna-tools
mmagnus / rna-tools
🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
rna-puzzle rna-pdb pdb rna rna-structure rosetta simrna bioinformatics python rna-tools
Language:Jupyter Notebook 179
fjossinet / RNArtist
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
bioinformatics java javafx-application kotlin rna rna-secondary-structure rna-structure
Language:Kotlin 162
jaswindersingh2 / SPOT-RNA
RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.
blstm-neural-networks bprna-dataset canonical-base-pairs deep-learning ensemble-model lone-pairs machine-learning multiplets-base-pairs noncanonical-base-pairs pdb-dataset pseudoknot-base-pairs resnet rna rna-secondary-structure rna-secondary-structure-prediction rna-structural-analysis rna-structure rna-structure-motifs tensorflow transfer-learning
Language:Perl 105
srnas / barnaba
Analyse Nucleic Acids Structure and Simulations with baRNAba
rna-structure python molecular-dynamics modeling rna rna-folding
Language:Jupyter Notebook 46
kiharalab / CryoREAD
CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
cryo-em dna-structure rna-structure
Language:Python 31
barricklab / ostir
Software for predicting translation initiation rates in bacteria
bioengineering rna-structure synthetic-biology
Language:Python 29
fjossinet / RNA-Science-Toolbox
A platform to do RNA science
rna-structure rna python bioinformatics
Language:Jupyter Notebook 27
fjossinet / RNArtistCore
A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.
bioinformatics drawing-algorithm dsl java kotlin plot-rna rna rna-molecule rna-secondary-structure rna-structure visualization
Language:Kotlin 27
TISIGNER-ReactJS
Gardner-BinfLab / TISIGNER-ReactJS
TISIGNER: Unleash the power of synthetic biology
webserver bioinformatics-tool rna-structure multiprocessing protein structural-biology biotechnology simulated-annealing translation-initiation-site solubility synthetic-biology
Language:JavaScript 27
MooersLab / jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
jupyter jupyter-notebook jupyterlab notebook python snippets grayscale ribbon-diagram protein-structure rna-structure dna-structure molecular-representation literate-programming moleclar-graphics pdb mmcif ligand biomolecular molecular
Language:HTML 25
MooersLab / EasyPyMOL
Script to facilitate the making of horizontal scripts
pymol pml horizontal-scripts molecular-graphics molecular-visuallization protein-structure molecular-artwork pymol-macro-language molecular-structures biomolecular-structures structural-bioinformatics ambient-occulsion black-and-white-cartoons coordinate-covalent-bonds rna-structure metal-coordination scripting tutorial-videos startup-aliases roundview
Language:Python 19
febos / SQUARNA
RNA secondary structure prediction tool
bioinformatics bioinformatics-tool biological-data-analysis biology prediction prediction-algorithm rna rna-secondary-structure rna-secondary-structure-prediction rna-structure rna-structure-prediction secondary-structure secondary-structure-prediction structural-biology structure structure-prediction alignment single-sequence 2d pseudoknot
Language:Jupyter Notebook 18
eternagame / EternaBench
Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.
rna-structure database ensemble
Language:Jupyter Notebook 17
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
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 pdb-files rna-pdb rna-structure rna-structure-prediction
Language:Emacs Lisp 13
cgoliver / Nussinov
Python implementation of Nussinov RNA folding algorithm and recursive backtrack.
nussinov rna-folding rna-structure dynamic-programming backtracking
Language:Python 10
ViennaRNA / RNAblueprint
RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints
rnablueprint-library riboswitch design rna-design inverse-folding rna-structure viennarna nupack
Language:C++ 10
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
david-bogdan-r / ARTEMIS
RNA/DNA 3D structure alignment tool
3d 3d-structure 3d-structure-alignment algorithm alignment bioinformatics bioinformatics-tool biological-data-analysis biology dna dna-3d-structure dna-structure nucleic-acid rna rna-3d-structure rna-structure structural-biology structure structure-alignment superposition
Language:Jupyter Notebook 8
nanobaselib / NanoBaseLib
[NeurIPS 2024] A Multi-task Benchmark Dataset for Nanopore Sequencing.
basecalling dna-sequences nanopore-sequencing rna-sequencing rna-structure
Language:Python 7
RNABioInfo / rna-interaction-format
RNA Interaction Format (RIF) with reference implementations in C++, JavaScript, and Python
bioinformatics cpp data-format data-storage data-structures database database-schema file-format interaction javascript json json-format json-schema python rna rna-structure schema specification transcriptomics
Language:C++ 7
fjossinet / kaknas
A JavaFX app to visualize RNA alignments from Rfam database.
bioinformatics javafx kotlin rna-alignment rna-structure visualization
Language:Kotlin 6
Ikarto / R4RNA
R4RNA visualisation package. Designed for visualization of RNA-RNA interactions and Genomic information from HiC data.
bioinformatics rna-structure
Language:R 6
BEAM-Labs / RTM-align
Official code of RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment.
rna-structure structure-alignment
Language:C++ 5
FelixErnst / Structstrings
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
sequences structures rna r bioconductor rna-structure rna-structural-analysis
Language:R 5
fjossinet / assemble2
Assemble2 allows you to design your RNA 2D structure interactively and to create and assemble the corresponding RNA 3D modules directly in UCSF Chimera
rna rna-structure visualization java pdb bioinformatics
Language:Java 5
noncodo / BigRedButton
Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.
bioinformatics rna-structure lncrna transcriptomics genome-annotation
Language:TeX 5
persalteas / RNANet
Multiscale dataset of non-coding RNA structures, including sequences, secondary structures, non-canonical interactions, 3D geometrical descriptors, and sequence homology.
rna rna-structure database rfam pdb
Language:Python 5
yiren-jian / CoT-RNA-Transfer
[ICPR 2024] Knowledge from Large-Scale Protein Contact Prediction Models can be Transferred to the Data-Scarce RNA Contact Prediction Task
computational-biology rna-structure transfer-learning
Language:Python 5
iyak / RNAelem
RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.
bioinformatics rna-structure motif-discovery
Language:C++ 4
mtw / Bio-RNA-RNAaliSplit
Split and decompose structural RNA multiple sequence alignments
rna rna-structure
Language:Perl 4
seqan / lara
LaRA 2: Lagrangian Relaxed structural Alignment
bioinformatics rna alignment rna-structure
Language:C++ 4
yikunpku / RESM
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
foundation-models language-model rna rna-rna-interactions rna-structure sirna transfer-learning zero-shot
Language:Python 3

rna-structure

baaihealth / OpenComplex

chaitjo / geometric-rna-design

mmagnus / rna-tools

fjossinet / RNArtist

jaswindersingh2 / SPOT-RNA

srnas / barnaba

kiharalab / CryoREAD

barricklab / ostir

fjossinet / RNA-Science-Toolbox

fjossinet / RNArtistCore

Gardner-BinfLab / TISIGNER-ReactJS

MooersLab / jupyterlabpymolpysnips

MooersLab / EasyPyMOL

febos / SQUARNA

eternagame / EternaBench

mmagnus / EvoClustRNA

mmagnus / emacs-pdb-mode

cgoliver / Nussinov

ViennaRNA / RNAblueprint

csfoo / contrafold-se

mmagnus / RNA-Puzzles-Standardized-Submissions

david-bogdan-r / ARTEMIS

nanobaselib / NanoBaseLib

RNABioInfo / rna-interaction-format

fjossinet / kaknas

Ikarto / R4RNA

BEAM-Labs / RTM-align

FelixErnst / Structstrings

fjossinet / assemble2

noncodo / BigRedButton

persalteas / RNANet

yiren-jian / CoT-RNA-Transfer

iyak / RNAelem

mtw / Bio-RNA-RNAaliSplit

seqan / lara

yikunpku / RESM