Trainable PyTorch framework for developing protein, RNA and complex models.
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Nov 13, 2024 - Python
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rna-structure
Here are 59 public repositories matching this topic...
gRNAde: Geometric Deep Learning for 3D RNA inverse design
pytorch rna-structure geometric-deep-learning graph-neural-networks pytorch-geometric inverse-design biomolecule-design
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Oct 6, 2024 - Jupyter Notebook
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
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Nov 24, 2023 - Kotlin
🔧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
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Dec 14, 2024 - Jupyter Notebook
RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.
machine-learning deep-learning tensorflow rna-structure rna resnet transfer-learning ensemble-model rna-structural-analysis blstm-neural-networks rna-secondary-structure rna-secondary-structure-prediction canonical-base-pairs noncanonical-base-pairs pseudoknot-base-pairs pdb-dataset bprna-dataset multiplets-base-pairs lone-pairs rna-structure-motifs
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Nov 15, 2022 - Perl
Analyse Nucleic Acids Structure and Simulations with baRNAba
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Mar 20, 2024 - Jupyter Notebook
CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
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Oct 14, 2024 - Python
A platform to do RNA science
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Mar 7, 2021 - Jupyter Notebook
A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.
visualization kotlin java bioinformatics dsl rna-structure rna drawing-algorithm rna-secondary-structure rna-molecule plot-rna
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Aug 27, 2024 - Kotlin
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
python snippets jupyter notebook pdb protein-structure jupyter-notebook literate-programming rna-structure jupyterlab grayscale molecular mmcif ligand biomolecular molecular-representation ribbon-diagram dna-structure moleclar-graphics
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May 9, 2024 - HTML
Software for predicting translation initiation rates in bacteria
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Nov 21, 2024 - Python
TISIGNER: Unleash the power of synthetic biology
structural-biology webserver synthetic-biology multiprocessing protein solubility rna-structure simulated-annealing translation-initiation-site biotechnology bioinformatics-tool
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Mar 3, 2023 - JavaScript
Evaluating RNA structure prediction using diverse thermodynamic prediction tasks and high-throughput datasets.
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Jun 10, 2022 - Jupyter Notebook
Script to facilitate the making of horizontal scripts
molecular-structures scripting protein-structure molecular-graphics pymol rna-structure pml structural-bioinformatics tutorial-videos horizontal-scripts molecular-visuallization molecular-artwork pymol-macro-language biomolecular-structures ambient-occulsion black-and-white-cartoons coordinate-covalent-bonds metal-coordination startup-aliases roundview
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May 25, 2024 - Python
RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io
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Nov 3, 2022 - Jupyter Notebook
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.
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Sep 15, 2022 - Emacs Lisp
Python implementation of Nussinov RNA folding algorithm and recursive backtrack.
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Oct 29, 2020 - Python
Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/archive/master.zip
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Apr 6, 2023 - Shell
RNAblueprint library for uniform sampling of RNA sequences given structural and sequence constraints
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Jul 29, 2024 - C++
CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data
machine-learning rna-structure conditional-random-fields rna-structure-prediction bioinformatics-algorithms
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Jul 11, 2024 - C++
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