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 254
fjossinet / RNArtist
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
kotlin javafx-application rna-structure rna java bioinformatics rna-secondary-structure
Language:Kotlin 158
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
bioinformatics pdb python rna rna-pdb rna-puzzle rna-structure rna-tools rosetta simrna
Language:Jupyter Notebook 145
chaitjo / geometric-rna-design
gRNAde: Geometric Deep Learning for 3D RNA inverse design
geometric-deep-learning graph-neural-networks inverse-design pytorch pytorch-geometric rna-structure biomolecule-design
Language:Jupyter Notebook 139
jaswindersingh2 / SPOT-RNA
RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.
rna rna-secondary-structure deep-learning transfer-learning ensemble-model resnet blstm-neural-networks tensorflow rna-secondary-structure-prediction canonical-base-pairs noncanonical-base-pairs pseudoknot-base-pairs pdb-dataset bprna-dataset multiplets-base-pairs lone-pairs machine-learning rna-structure rna-structural-analysis rna-structure-motifs
Language:Perl 93
srnas / barnaba
Analyse Nucleic Acids Structure and Simulations with baRNAba
rna-structure python molecular-dynamics modeling rna rna-folding
Language:Jupyter Notebook 36
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 28
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.
kotlin visualization java bioinformatics rna rna-structure dsl drawing-algorithm plot-rna rna-molecule rna-secondary-structure
Language:Kotlin 26
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 22
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 18
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 15
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 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
barricklab / ostir
Software for predicting translation initiation rates in bacteria
synthetic-biology bioengineering rna-structure
Language:Python 12
eternagame / EternaBench
Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.
rna-structure database ensemble
Language:Jupyter Notebook 12
cgoliver / Nussinov
Python implementation of Nussinov RNA folding algorithm and recursive backtrack.
nussinov rna-folding rna-structure dynamic-programming backtracking
Language:Python 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
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++ 8
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++ 8
fjossinet / kaknas
A JavaFX app to visualize RNA alignments from Rfam database.
rna-structure rna-alignment bioinformatics kotlin javafx visualization
Language:Kotlin 6
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++ 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
Ikarto / R4RNA
R4RNA visualisation package. Designed for visualization of RNA-RNA interactions and Genomic information from HiC data.
bioinformatics rna-structure
Language:R 5
yiren-jian / CoT-RNA-Transfer
[Under Review] Knowledge from Large-Scale Protein Contact Prediction Models can be Transferred to the Data-Scarce RNA Contact Prediction Task
computational-biology transfer-learning rna-structure
Language:Python 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 4
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 4
mtw / Bio-RNA-RNAaliSplit
Split and decompose structural RNA multiple sequence alignments
rna rna-structure
Language:Perl 4
noncodo / BigRedButton
Pipeline for the unsupervised clustering of homologous RNA structure motifs from sequencing data.
bioinformatics rna-structure lncrna transcriptomics genome-annotation
Language:TeX 4
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 4
seqan / lara
LaRA 2: Lagrangian Relaxed structural Alignment
bioinformatics rna alignment rna-structure
Language:C++ 4
amchakra / tosca
Nextflow analysis pipeline for hiCLIP and proximity ligation sequencing data
bioinformatics nextflow-pipeline rna-structure hiclip proximity-ligation
Language:Nextflow 3
HosnaJabbari / Iterative-HFold
RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding
rna-folding rna-structure-prediction hfold hfold-iterative iterative-hfold rna rna-structure pseudoknot-structures
Language:C++ 3
TIsigner
Gardner-BinfLab / TIsigner
Translation Initiation coding region designer
webserver bioinformatics rna-structure multiprocessing protein structural-biology biotechnology simulated-annealing translation-initiation-site
Language:CSS 2
HosnaJabbari / DinoKnot
RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding
rna-structure-prediction rna-folding hfold hfold-interacting interacting-hfold rna rna-structure pseudoknot-structures
Language:C++ 2
s-will / BiAlign
Bialignment of RNAs and proteins
bioinformatics alignment rna-structure protein-structure
Language:Python 2

rna-structure

baaihealth / OpenComplex

fjossinet / RNArtist

mmagnus / rna-tools

chaitjo / geometric-rna-design

jaswindersingh2 / SPOT-RNA

srnas / barnaba

kiharalab / CryoREAD

fjossinet / RNA-Science-Toolbox

fjossinet / RNArtistCore

MooersLab / jupyterlabpymolpysnips

Gardner-BinfLab / TISIGNER-ReactJS

MooersLab / EasyPyMOL

mmagnus / emacs-pdb-mode

mmagnus / EvoClustRNA

barricklab / ostir

eternagame / EternaBench

cgoliver / Nussinov

mmagnus / RNA-Puzzles-Standardized-Submissions

csfoo / contrafold-se

ViennaRNA / RNAblueprint

fjossinet / kaknas

RNABioInfo / rna-interaction-format

BEAM-Labs / RTM-align

Ikarto / R4RNA

yiren-jian / CoT-RNA-Transfer

FelixErnst / Structstrings

fjossinet / assemble2

mtw / Bio-RNA-RNAaliSplit

noncodo / BigRedButton

persalteas / RNANet

seqan / lara

amchakra / tosca

HosnaJabbari / Iterative-HFold

Gardner-BinfLab / TIsigner

HosnaJabbari / DinoKnot

s-will / BiAlign