Kihara Protein Bioinformatics Laboratory (@kiharalab)
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Top repositories

1

ACC-UNet

ACC-UNet is A Completely Convolutional UNet model inspired from transformer-based UNets
Python
99
star
2

GNN_DOVE

Code for "Protein Docking Model Evaluation by Graph Neural Networks"
Python
57
star
3

DOVE

A Deep-learning based dOcking decoy eValuation mEthod
Python
54
star
4

CryoREAD

CryoREAD: a computational tool using deep learning to automatically build full DNA/RNA atomic structure from cryo-EM map.
Python
28
star
5

DiffModeler

DiffModeler: a diffusion model based protein complex structure modeling tool.
Python
27
star
6

Emap2secPlus

Emap2sec+: Detecting Protein and DNA/RNA Structures in Cryo-EM Maps of Intermediate Resolution Using Deep Learning
Jupyter Notebook
17
star
7

Emap2sec

Emap2sec is a computational tool to identify protein secondary structures
Jupyter Notebook
16
star
8

Distance-AF

Public version for Distance-AF
Python
16
star
9

DAQ

DAQ: Residue-Wise Local Quality Estimation for Protein Models from Cryo-EM Maps
C
13
star
10

DeepMainMast

DeepMainmast
C
11
star
11

GO2Sum

GO2Sum is a deep learning based summarizer that generates human-readable summaries for GO term annotations made by protein function prediction methods.
Jupyter Notebook
10
star
12

VESPER

C
10
star
13

RL-MLZerD

C
10
star
14

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.
Jupyter Notebook
10
star
15

Flex-LZerD

Python
9
star
16

Domain-PFP

Domain-PFP is a self-supervised method to predict protein functions from the domains
Jupyter Notebook
8
star
17

ContactGAN

Contact map denoising using GANs
Python
8
star
18

3d-af_surfer

Python
7
star
19

DAQ-Refine

Jupyter Notebook
6
star
20

DistPepFold

Public version for DistPepFold
Python
5
star
21

AFM-RL

Python
5
star
22

NNTox

Python
4
star
23

idp_lzerd

Modeling disordered protein interactions from biophysical principles
Python
4
star
24

OC_Finder

Python
4
star
25

2DKD

Two-Dimensional Krawtchouk Descriptors for Content Based Local Image Search
MATLAB
4
star
26

contactPFP

Protein function prediction based on predicted residue-residue contacts
Python
3
star
27

NaviGO

Tools for analyzing and visualizing Gene Ontology gene function terms
Perl
3
star
28

MAINMASTplugin

Chimera plugin for MAINMAST
Objective-C
3
star
29

AttentiveDist

Python
3
star
30

NuFold

NuFold: End-to-End Approach for RNA Tertiary Structure Prediction with Flexible Nucleobase Center Representation
Jupyter Notebook
3
star
31

Attention_AD

Attention LSTM code for "Activation of gene expression by nucleosome detergents"
Python
2
star
32

ComplexModeler

Python
2
star
33

MarkovFit

C
1
star
34

MASQ_PPI

Python
1
star
35

GNN_pocket

The project of pocket prediction based on GNN model
C
1
star
36

MAINMASTseg

Automated Segmentation Program for EM map with symmetry
C
1
star