rna-structure

There are 59 repositories under rna-structure topic.

  • OpenComplex

    baaihealth/OpenComplex

    Trainable PyTorch framework for developing protein, RNA and complex models.

    Language:Python26717133

  • chaitjo/geometric-rna-design

    gRNAde: Geometric Deep Learning for 3D RNA inverse design

    Language:Jupyter Notebook16411816

  • fjossinet/RNArtist

    With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...

    Language:Kotlin15861910
  • 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

    Language:Jupyter Notebook1531011942

  • jaswindersingh2/SPOT-RNA

    RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

    Language:Perl9762132

  • srnas/barnaba

    Analyse Nucleic Acids Structure and Simulations with baRNAba

    Language:Jupyter Notebook41112815

  • kiharalab/CryoREAD

    CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

    Language:Python28444

  • fjossinet/RNA-Science-Toolbox

    A platform to do RNA science

    Language:Jupyter Notebook27629

  • 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:Kotlin26265

  • MooersLab/jupyterlabpymolpysnips

    Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

    Language:HTML24215

  • barricklab/ostir

    Software for predicting translation initiation rates in bacteria

    Language:Python19499
  • TISIGNER-ReactJS

    Gardner-BinfLab/TISIGNER-ReactJS

    TISIGNER: Unleash the power of synthetic biology

    Language:JavaScript19647

  • eternagame/EternaBench

    Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.

    Language:Jupyter Notebook162203

  • MooersLab/EasyPyMOL

    Script to facilitate the making of horizontal scripts

    Language:Python154918

  • 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 Lisp14617

  • mmagnus/EvoClustRNA

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

    Language:Jupyter Notebook14276

  • cgoliver/Nussinov

    Python implementation of Nussinov RNA folding algorithm and recursive backtrack.

    Language:Python10217

  • csfoo/contrafold-se

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

    Language:C++9333

  • 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:Shell9497

  • ViennaRNA/RNAblueprint

    RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints

    Language:C++9733

  • fjossinet/kaknas

    A JavaFX app to visualize RNA alignments from Rfam database.

    Language:Kotlin6200

  • Ikarto/R4RNA

    R4RNA visualisation package. Designed for visualization of RNA-RNA interactions and Genomic information from HiC data.

    Language:R6230

  • RNABioInfo/rna-interaction-format

    RNA Interaction Format (RIF) with reference implementations in C++, JavaScript, and Python

    Language:C++6410

  • 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++5000

  • 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:Java5301

  • 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:Python5201

  • FelixErnst/Structstrings

    :package: Structstrings: implementation of Biostrings to work with dot bracket annotations

    Language:R4210

  • mtw/Bio-RNA-RNAaliSplit

    Split and decompose structural RNA multiple sequence alignments

    Language:Perl4310

  • noncodo/BigRedButton

    Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.

    Language:TeX4411

  • persalteas/RNANet

    Multiscale dataset of non-coding RNA structures, including sequences, secondary structures, non-canonical interactions, 3D geometrical descriptors, and sequence homology.

    Language:Python4201

  • seqan/lara

    LaRA 2: Lagrangian Relaxed structural Alignment

    Language:C++4533

  • amchakra/tosca

    Nextflow analysis pipeline for hiCLIP and proximity ligation sequencing data

    Language:Nextflow31122

  • HosnaJabbari/Iterative-HFold

    RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding

    Language:C++3324

  • iyak/RNAelem

    RNAelem is a tool for learning secondary structural motifs from a set of RNA sequences.

    Language:C++3200
  • TIsigner

    Gardner-BinfLab/TIsigner

    Translation Initiation coding region designer

    Language:CSS2213

  • JLP-BioInf/rnaCrosslinkNF

    Pre-processing pipeline for RNA crosslinking and High throughput sequencing data.

    Language:R2100