Kihara Protein Bioinformatics Laboratory

ACC-UNet

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

GNN_DOVE

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

DOVE

A Deep-learning based dOcking decoy eValuation mEthod

CryoREAD

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

DiffModeler

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

Emap2sec

Emap2sec is a computational tool to identify protein secondary structures

Emap2secPlus

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

Distance-AF

Public version for Distance-AF

DAQ

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

RL-MLZerD

Flex-LZerD

GO2Sum

GO2Sum is a deep learning based summarizer that generates human-readable summaries for GO term annotations made by protein function prediction methods.

VESPER

DeepMainMast

DeepMainmast

Domain-PFP

Domain-PFP is a self-supervised method to predict protein functions from the domains

EM-GAN

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.

DAQ-Refine

AFM-RL

DistPepFold

Public version for DistPepFold

OC_Finder

contactPFP

Protein function prediction based on predicted residue-residue contacts

Attention_AD

Attention LSTM code for "Activation of gene expression by nucleosome detergents"

NuFold

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

ComplexModeler

MAINMASTseg

Automated Segmentation Program for EM map with symmetry

AF2_Distaf

Embedding generation for Distance-AF using full MSA

ColabFold

Making Protein folding accessible to all!

ColabFold_Distaf

Embedding generation for Distance-AF

ColabFoldDAQ

Making Protein folding accessible to all!

GNN-TAD