Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
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Updated
May 28, 2024 - Python
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
nucleic acid folding
Code for our Nature Scientific Reports paper "A universal framework for accurate and efficient geometric deep learning of molecular systems"
RiboNucleic Acid (RNA) Language Model
Alignment of RNAs
DNA/RNA folding in Nim
Julia interface to ViennaRNA for RNA structure prediction and analysis
RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io
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.
A gym environment for the research which apply the reinforcement learning algorithm to the RNA structure prediction
Curated structures submitted to the RNA-Puzzles experiment. Download as a zip file https://github.com/mmagnus/RNA-Puzzles-submission/archive/master.zip
CONTRAfold-SE - Learning RNA secondary structure (only) from structure probing data
Julia interface to LinearFold RNA structure prediction programs: LinearFold, LinearPartition, LinearSampling, and LinearTurboFold
locality-aware invariant Point Attention-based RNA ScorEr
RNA Pseudoknotted Secondary Structure Prediction Using Relaxed Hierarchical Folding
MFE method for predicting the psuedoknotted secondary structures of RNA sequences.
RNA/DNA/PMO Pseudoknotted Secondary Structure Interaction Prediction Using Relaxed Hierarchical Folding
Python bindings to use the historical GTFold library natively in the RNADB construction script and natively with Python3. See the WIKI pages for documentation and installation notes.
Visualizes the secondary structure of RNA using Verna
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