Topic: "rna-structure"
baaihealth/OpenComplex
Trainable PyTorch framework for developing protein, RNA and complex models.
Language: Python - Size: 14.6 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 264 - Forks: 33
chaitjo/geometric-rna-design
gRNAde: Geometric Deep Learning for 3D RNA inverse design (ICLR 2025 Spotlight)
Language: Jupyter Notebook - Size: 305 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 190 - Forks: 19
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
Language: Jupyter Notebook - Size: 114 MB - Last synced at: 13 days ago - Pushed at: about 1 month ago - Stars: 173 - Forks: 43
fjossinet/RNArtist
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
Language: Kotlin - Size: 31.7 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 158 - Forks: 10
jaswindersingh2/SPOT-RNA
RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.
Language: Perl - Size: 6.82 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 81 - Forks: 30
srnas/barnaba
Analyse Nucleic Acids Structure and Simulations with baRNAba
Language: Jupyter Notebook - Size: 42.1 MB - Last synced at: 11 days ago - Pushed at: about 1 year ago - Stars: 42 - Forks: 16
kiharalab/CryoREAD
CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
Language: Python - Size: 398 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 28 - Forks: 4
fjossinet/RNA-Science-Toolbox
A platform to do RNA science
Language: Jupyter Notebook - Size: 18.4 MB - Last synced at: 17 days ago - Pushed at: about 4 years ago - Stars: 27 - Forks: 9
fjossinet/RNArtistCore
A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.
Language: Kotlin - Size: 25.8 MB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 26 - Forks: 6
MooersLab/jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
Language: HTML - Size: 8.76 MB - Last synced at: 25 days ago - Pushed at: 12 months ago - Stars: 24 - Forks: 5
barricklab/ostir
Software for predicting translation initiation rates in bacteria
Language: Python - Size: 6.84 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 22 - Forks: 9
Gardner-BinfLab/TISIGNER-ReactJS
TISIGNER: Unleash the power of synthetic biology
Language: JavaScript - Size: 160 MB - Last synced at: 9 months ago - Pushed at: about 2 years ago - Stars: 18 - Forks: 7
MooersLab/EasyPyMOL
Script to facilitate the making of horizontal scripts
Language: Python - Size: 646 KB - Last synced at: 25 days ago - Pushed at: 11 months ago - Stars: 16 - Forks: 18
eternagame/EternaBench 📦
Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.
Language: Jupyter Notebook - Size: 789 MB - Last synced at: 12 days ago - Pushed at: almost 3 years ago - Stars: 16 - Forks: 3
febos/SQUARNA
RNA secondary structure prediction tool
Language: Jupyter Notebook - Size: 162 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 14 - 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: 12 months ago - Pushed at: over 2 years ago - Stars: 14 - Forks: 5
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.
Language: Emacs Lisp - Size: 351 KB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 6
cgoliver/Nussinov
Python implementation of Nussinov RNA folding algorithm and recursive backtrack.
Language: Python - Size: 2.93 KB - Last synced at: 19 days ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 7
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: 12 months ago - Pushed at: about 2 years ago - Stars: 9 - Forks: 7
ViennaRNA/RNAblueprint
RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints
Language: C++ - Size: 3.75 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 8 - Forks: 3
csfoo/contrafold-se
CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data
Language: C++ - Size: 168 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 8 - Forks: 4
RNABioInfo/rna-interaction-format
RNA Interaction Format (RIF) with reference implementations in C++, JavaScript, and Python
Language: C++ - Size: 298 KB - Last synced at: 2 days ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 0
fjossinet/kaknas
A JavaFX app to visualize RNA alignments from Rfam database.
Language: Kotlin - Size: 3.91 KB - Last synced at: 17 days ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0
FelixErnst/Structstrings
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
Language: R - Size: 399 KB - Last synced at: 17 days ago - Pushed at: 6 months ago - Stars: 5 - Forks: 0
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
Language: Python - Size: 149 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 5 - Forks: 1
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.
Language: C++ - Size: 78.1 KB - Last synced at: 3 months ago - Pushed at: 11 months ago - Stars: 5 - Forks: 0
noncodo/BigRedButton
Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.
Language: TeX - Size: 34.2 MB - Last synced at: 11 days ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 1
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
Language: Java - Size: 30.9 MB - Last synced at: 17 days ago - Pushed at: about 7 years ago - Stars: 5 - Forks: 1
seqan/lara
LaRA 2: Lagrangian Relaxed structural Alignment
Language: C++ - Size: 457 KB - Last synced at: 16 days ago - Pushed at: over 3 years ago - Stars: 4 - Forks: 3
mtw/Bio-RNA-RNAaliSplit
Split and decompose structural RNA multiple sequence alignments
Language: Perl - Size: 149 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 0
amchakra/tosca
Nextflow analysis pipeline for hiCLIP and proximity ligation sequencing data
Language: Nextflow - Size: 406 KB - Last synced at: 6 days ago - Pushed at: 7 days ago - Stars: 3 - Forks: 3
TheCOBRALab/Iterative-HFold
RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding
Language: C++ - Size: 5.71 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 5
Ikarto/R4RNA
R4RNA visualisation package. Designed for visualization of RNA-RNA interactions and Genomic information from HiC data.
Language: R - Size: 12.3 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 0
JLP-BioInf/rnaCrosslinkNF
Pre-processing pipeline for RNA crosslinking and High throughput sequencing data.
Language: R - Size: 38.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
TheCOBRALab/DinoKnot
RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding
Language: C++ - Size: 13 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 4
iyak/RNAelem
RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.
Language: C++ - Size: 44 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0
Gardner-BinfLab/TIsigner
Translation Initiation coding region designer
Language: CSS - Size: 3.86 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 2
naotohori/TIS2AA
Construct atomistic (AA) model from Three-Interaction-Site (TIS) coarse-grained model of RNA/DNA
Language: Python - Size: 3.29 MB - Last synced at: 5 months ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1
s-will/BiAlign
Bialignment of RNAs and proteins
Language: Python - Size: 145 KB - Last synced at: 18 days ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 0
pmenzel/RILogo
Visualising RNA-RNA interactions
Language: C++ - Size: 54.7 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years 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: about 1 month ago - Pushed at: about 7 years ago - Stars: 2 - Forks: 1
TheCOBRALab/HFold
RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding
Language: C - Size: 20.8 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 4
david-bogdan-r/ARTEM
RNA/DNA 3D structure alignment tool
Language: Python - Size: 10.5 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
Oriaooo/awesome-rna-3d-structure-prediction-models
A curated list of deep learning methods to predict RNA 3D structure.
Size: 31.3 KB - Last synced at: 12 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0
Gardner-BinfLab/TIsigner_paper_2019
Code related to TIsigner manuscript and webserver
Language: Jupyter Notebook - Size: 21.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
Bhattacharya-Lab/RNAmark
The landscape of RNA 3D structure modeling with transformer networks
Language: Shell - Size: 44 MB - Last synced at: 4 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0
kris96tian/dsa_cpp
Bioinformatics Data Structures & Algorithms [such as the Q-Gram Index, scoring alignments , rna-structure prediction, generating the BLAST-Ńeighborhood and more.]
Language: C++ - Size: 203 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
MooersLab/rstudiopymolpysnips
PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.
Language: Vim Snippet - Size: 224 MB - Last synced at: 24 days ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0
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: 1.91 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
fjossinet/RNArtistFX
JavaFX widgets to visualize and manipulate RNA structures.
Language: Kotlin - Size: 2.93 KB - Last synced at: 2 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0
persalteas/RNANet
Multiscale dataset of non-coding RNA structures, including sequences, secondary structures, non-canonical interactions, 3D geometrical descriptors, and sequence homology.
Language: Python - Size: 3.62 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1
rna-oop/2425-m1-geniomhe-group-6
OOP2 labs: allows easy manipulation and study of RNA sequences spatially
Language: Jupyter Notebook - Size: 60.3 MB - Last synced at: 8 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 1
febos/SQUARNA-data
SQUARNA benchmark data
Language: Jupyter Notebook - Size: 105 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - Forks: 0
yoobright/ufold_demo
extremely simple UFold demo
Language: Python - Size: 0 Bytes - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
mzhang8132/RNA_Structure_Visualizer
RNA secondary structure predictor based on the Nussinov algorithm that generates all optimal structures utilizing the Wuchty algorithm with visualization of the best predicted secondary structure.
Language: Jupyter Notebook - Size: 19.5 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0
rouskinlab/seismic-graph Fork of rouskinlab/dreem
Plotting engine for SEISMIC-RNA
Language: Jupyter Notebook - Size: 106 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
f1lem0n/transfold
Deciphering the link between transcript and protein structure
Language: Python - Size: 13.7 MB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
EfeErkan/RNA_Folding_Linear_Programing
Solving RNA Folding Problems with Linear/Integer Programming
Language: Python - Size: 945 KB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
seqan/mars
Motif-based aligned RNA searcher
Language: C++ - Size: 7.71 MB - Last synced at: about 2 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 2
dmancilla85/r-laslo
Data cleaning and analysis of LASLO results
Language: R - Size: 6.85 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
gmagannaDevelop/ARN.py
Final Project : Algorithms and Object-Oriented programming. Secodary structure of ARN molecules
Language: Python - Size: 2 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
Bader-Research/gtfold Fork of gtfold/gtfold
GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.
Language: C++ - Size: 9.54 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
kubawajs/PyRy3D-DisplayRestraints
Extension for creating visualizations of distance restraints in PyRy3D Chimera Extension
Language: Python - Size: 1.85 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0
mkarlik93/ADPB-projekt Fork of GruA/ADPB-projekt
Architecture of Large Projects in Bioinformatics (University project)
Language: Python - Size: 2.33 MB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0
