TheCOBRALab/HFold

RNA Pseudoknotted Secondary Structure Prediction Using Strict Hierarchical Folding

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srnas/barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba

Language: Jupyter Notebook - Size: 42.1 MB - Last synced at: 15 days ago - Pushed at: about 1 year ago - Stars: 42 - Forks: 16

GiatrasKon/Algorithms-in-Structural-Bioinformatics-Assignments

Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.

Language: Jupyter Notebook - Size: 6.61 MB - Last synced at: 29 days ago - Pushed at: 5 months ago - Stars: 1 - 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/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 2 months ago - Stars: 2 - Forks: 4

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 2 months ago - Stars: 3 - Forks: 5

marcom/ViennaRNA.jl

Julia interface to ViennaRNA for RNA structure prediction and analysis

Language: Julia - Size: 328 KB - Last synced at: 21 days ago - Pushed at: about 1 year ago - Stars: 22 - Forks: 1

Koeng101/dnadesign

A Go package for designing DNA.

Language: Go - Size: 36.8 MB - Last synced at: 16 days ago - Pushed at: 5 months ago - Stars: 30 - Forks: 1

lemerleau/RAFFT

RAFFT: RNA structure and folding dynamics predictions using the fast Fourier transform

Language: Python - Size: 83.5 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 1

Hori-Lab/SIS

Coarse-grained molecular dynamics simulation with the Single-Interaction-Site RNA model

Language: Fortran - Size: 1.23 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 3 - Forks: 0

marcom/FoldRNA.jl

Nucleic acid secondary structure prediction and analysis

Language: Julia - Size: 118 KB - Last synced at: 27 days ago - Pushed at: 5 months ago - Stars: 5 - Forks: 1

cgoliver/Nussinov

Python implementation of Nussinov RNA folding algorithm and recursive backtrack.

Language: Python - Size: 2.93 KB - Last synced at: 23 days ago - Pushed at: over 4 years ago - Stars: 10 - Forks: 7

vercetti322/RNA-Folding

This is a dynamic programming implementation with an SDL visualization of conversion from mRNA to most optimal secondary structure (most number of base pairs).

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Lattice-Automation/seqfold

nucleic acid folding

Language: Python - Size: 136 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 79 - Forks: 12

Saphereye/RNA-folding-simulation

Implementation and visualization of dynamic programming based RNA secondary structure approximation

Language: C++ - Size: 1.5 MB - Last synced at: 2 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

marcom/LinearFold.jl

Julia interface to LinearFold RNA structure prediction programs: LinearFold, LinearPartition, LinearSampling, and LinearTurboFold

Language: Julia - Size: 36.1 KB - Last synced at: 27 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 0

nlabrad/CIMS-Cyanobacterial-ITS-motif-slicer

A tool to identify and extract the commonly used ITS folding motifs from a 16s-23s rRNA sequence.

Language: Python - Size: 6.06 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 1

marcom/RNAstructure.jl

Julia interface to the RNAstructure program suite for RNA structure prediction and analysis

Language: Julia - Size: 89.8 KB - Last synced at: 27 days ago - Pushed at: over 1 year ago - Stars: 10 - Forks: 1

LedaKatopodi/rna-folding

RNA folding; implementation of the Zuker algorithm.

Language: Jupyter Notebook - Size: 1.23 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

GeoRouv/RNA-folding

🧬 Zuker: An RNA secondary structure prediction algorithm

Language: Jupyter Notebook - Size: 115 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 3 - Forks: 1

RFOLD/RhoFold

Open source code for RhoFold: Fast and Accurate RNA 3D Structure Prediction with Deep Learning.

Language: Python - Size: 30.8 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 39 - Forks: 6

ChristinaAndrinopoyloy/Algorithms_in_Structural_Biology

2 homeworks for "Algorithms in Structural Biology" Master course of Data Science and Information Technologies (DSIT)

Language: Jupyter Notebook - Size: 8.68 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 0

ChevronOne/Tools-For-Computational-Biology

Tools For Computational Biology

Language: C++ - Size: 2.81 MB - Last synced at: about 2 years ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 1

andriusbern/RNAgent

RNA design tool that utilizes reinforcement learning

Language: Python - Size: 105 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Po0ria/BPMax

Implementation of BPMax algorithm using AlphaZ Framework

Size: 35.2 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

juvion/EBMonteCarlo

Language: C++ - Size: 338 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

YannDubs/FourRussiansRNA

Faster algorithms for RNA-folding using the Four-Russians method

Language: C++ - Size: 1.74 MB - Last synced at: about 1 month ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 1

raph-m/RNA-folding Fork of gabmis/rna-folding

RNA folding project in C++

Language: C++ - Size: 3.91 KB - Last synced at: about 2 years ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 1