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@kiharalab

Kihara Protein Bioinformatics Laboratory

Software developed in the Kihara Lab

Popular repositories Loading

  1. ACC-UNet ACC-UNet Public

    ACC-UNet is A Completely Convolutional UNet model inspired from transformer-based UNets

    Python 123 16

  2. GNN_DOVE GNN_DOVE Public

    Code for "Protein Docking Model Evaluation by Graph Neural Networks"

    Python 59 21

  3. DiffModeler DiffModeler Public

    DiffModeler: a diffusion model based protein complex structure modeling tool.

    Python 59 5

  4. DOVE DOVE Public

    A Deep-learning based dOcking decoy eValuation mEthod

    Python 57 12

  5. NuFold NuFold Public

    NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation

    Jupyter Notebook 48 7

  6. CryoREAD CryoREAD Public

    CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.

    Python 32 5

Repositories

Showing 10 of 49 repositories
  • DiffModeler Public

    DiffModeler: a diffusion model based protein complex structure modeling tool.

    kiharalab/DiffModeler’s past year of commit activity
    Python 59 5 0 0 Updated Jan 12, 2026
  • queryome Public

    An Agentic AI system for Biomedical Deep Research

    kiharalab/queryome’s past year of commit activity
    Python 1 GPL-3.0 0 0 0 Updated Dec 16, 2025
  • Emap2secPlus Public

    Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning

    kiharalab/Emap2secPlus’s past year of commit activity
    Jupyter Notebook 18 GPL-3.0 9 0 0 Updated Nov 21, 2025
  • NuFold Public

    NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation

    kiharalab/NuFold’s past year of commit activity
    Jupyter Notebook 48 GPL-3.0 7 0 0 Updated Oct 31, 2025
  • SHREC2025 Public
    kiharalab/SHREC2025’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Oct 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.

    kiharalab/DMcloudComplex’s past year of commit activity
    Python 0 0 0 0 Updated Oct 17, 2025
  • DAQ Public

    DAQ: Residue-Wise Local Quality Estimation for Protein Models from Cryo-EM Maps

    kiharalab/DAQ’s past year of commit activity
    C 17 GPL-3.0 2 0 0 Updated Oct 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.

    kiharalab/DMCloud’s past year of commit activity
    Python 0 GPL-3.0 0 0 0 Updated Aug 26, 2025
  • Distance-AF Public

    Public version for Distance-AF

    kiharalab/Distance-AF’s past year of commit activity
    Python 30 GPL-3.0 5 1 0 Updated Aug 17, 2025
  • DistPepFold Public

    Public version for DistPepFold

    kiharalab/DistPepFold’s past year of commit activity
    Python 10 GPL-3.0 1 0 0 Updated Jul 17, 2025

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