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@kiharalab Kihara Protein Bioinformatics Laboratory

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    49 repositories

    • queryome

      Public
      An Agentic AI system for Biomedical Deep Research
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Dec 16, 2025Dec 16, 2025

    • DiffModeler

      Public
      DiffModeler: a diffusion model based protein complex structure modeling tool.
      deep-learningprotein-structurecryo-emstructure-determinationdiffusion-modelstructure-modeling
      Python
      •5•59•0•0•Updated Dec 8, 2025Dec 8, 2025

    • Emap2secPlus

      Public
      Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning
      cryo-em
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •9•18•0•0•Updated Nov 21, 2025Nov 21, 2025

    • NuFold

      Public
      NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•48•0•0•Updated Oct 31, 2025Oct 31, 2025

    • SHREC2025

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Oct 18, 2025Oct 18, 2025

    • DMcloudComplex

      Public
      DMcloudComplex is a macromolecular structure modeling tool using point cloud matching with diffusion model and 3D U-net (CryoREAD) for cryo-EM maps at 3-10A resolution.
      Python
      •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

    • DAQ

      Public
      DAQ: Residue-Wise Local Quality Estimation for Protein Models from Cryo-EM Maps
      cryo-em
      C
      •
      GNU General Public License v3.0
      •2•17•0•0•Updated Oct 7, 2025Oct 7, 2025

    • DMCloud

      Public
      DMcloud is a macromolecular structure modeling tool using point cloud matching with diffusion model for cryo-EM maps at 3-15A resolution.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 26, 2025Aug 26, 2025

    • Distance-AF

      Public
      Public version for Distance-AF
      Python
      •
      GNU General Public License v3.0
      •5•30•1•0•Updated Aug 17, 2025Aug 17, 2025

    • DistPepFold

      Public
      Public version for DistPepFold
      Python
      •
      GNU General Public License v3.0
      •1•9•0•0•Updated Jul 17, 2025Jul 17, 2025

    • DAQ-Refine

      Public
      Jupyter Notebook
      •1•6•0•0•Updated Apr 15, 2025Apr 15, 2025

    • EQAFold_public

      Public
      Public Release of EQAfold
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Mar 30, 2025Mar 30, 2025

    • EM-GAN

      Public
      EM-GAN is a computational tool, which enables capturing protein structure information from cryo-EM maps more effectively than raw maps. It is based on 3D deep learning. It is aimed to help protein structure modeling from cryo-EM maps.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•17•3•0•Updated Mar 4, 2025Mar 4, 2025

    • OC_Finder

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•6•0•0•Updated Jan 24, 2025Jan 24, 2025

    • CryoREAD

      Public
      CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
      rna-structurecryo-emdna-structure
      Python
      •5•32•0•0•Updated Oct 14, 2024Oct 14, 2024

    • GO2Sum_Server

      Public
      The code for GO2Sum server
      0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • ComplexModeler

      Public
      Python
      •0•5•0•0•Updated Sep 7, 2024Sep 7, 2024

    • AF2_Distaf

      Public
      Embedding generation for Distance-AF using full MSA
      Python
      •
      Apache License 2.0
      •2.5k•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • ColabFoldDAQ

      Public
      Making Protein folding accessible to all!
      Jupyter Notebook
      •
      MIT License
      •694•0•0•1•Updated Aug 17, 2024Aug 17, 2024

    • DeepMainMast

      Public
      DeepMainmast
      protein-structurecryo-emstructure-modeling
      C
      •
      GNU General Public License v3.0
      •2•15•0•1•Updated Aug 12, 2024Aug 12, 2024

    • Emap2sec

      Public
      Emap2sec is a computational tool to identify protein secondary structures
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •7•16•2•0•Updated Jul 31, 2024Jul 31, 2024

    • VESPER

      Public
      C
      •
      GNU General Public License v3.0
      •2•12•0•0•Updated Jul 31, 2024Jul 31, 2024

    • ColabFold_Distaf

      Public
      Embedding generation for Distance-AF
      Jupyter Notebook
      •
      MIT License
      •694•0•0•0•Updated Apr 11, 2024Apr 11, 2024

    • GO2Sum

      Public
      GO2Sum is a deep learning based summarizer that generates human-readable summaries for GO term annotations made by protein function prediction methods.
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •1•16•2•1•Updated Mar 27, 2024Mar 27, 2024

    • GNN-TAD

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 20, 2024Feb 20, 2024

    • AFM-RL

      Public
      Python
      •1•5•1•0•Updated Jan 19, 2024Jan 19, 2024

    • ColabFold

      Public
      Making Protein folding accessible to all!
      Jupyter Notebook
      •
      MIT License
      •694•0•0•0•Updated Jan 9, 2024Jan 9, 2024

    • Domain-PFP

      Public
      Domain-PFP is a self-supervised method to predict protein functions from the domains
      protein-function-prediction
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•14•3•0•Updated Nov 1, 2023Nov 1, 2023

    • ACC-UNet

      Public
      ACC-UNet is A Completely Convolutional UNet model inspired from transformer-based UNets
      medical-imagingimage-segmentationunetconvolutional-neural-network
      Python
      •
      GNU General Public License v3.0
      •16•123•5•0•Updated Oct 16, 2023Oct 16, 2023

    • Attention_AD

      Public
      Attention LSTM code for "Activation of gene expression by nucleosome detergents"
      Python
      •0•2•0•0•Updated May 12, 2023May 12, 2023