westlake-repl/SaprotHub

Making Protein Modeling Accessible to All Biologists

Language: Jupyter Notebook - Size: 91.3 MB - Last synced at: about 7 hours ago - Pushed at: about 8 hours ago - Stars: 106 - Forks: 12

hotdogee/annotate-ui

Protein Function Prediction using Deep Learning

Language: Vue - Size: 8.9 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

jiaqingxie/DeepProtein

Code base for the paper DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning, Accepted @ Bioinformatics 2025

Language: Jupyter Notebook - Size: 201 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 24 - Forks: 2

microsoft/protein-uq

Benchmarking uncertainty quantification methods on proteins.

Language: Jupyter Notebook - Size: 131 MB - Last synced at: about 24 hours ago - Pushed at: 3 months ago - Stars: 20 - Forks: 4

kexinhuang12345/DeepPurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

Language: Jupyter Notebook - Size: 14.5 MB - Last synced at: 18 days ago - Pushed at: 11 months ago - Stars: 1,028 - Forks: 282

primaryodors/primarydock

PrimaryOdors.org molecular docker.

Language: C++ - Size: 739 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 7 - Forks: 4

J-SNACKKB/FLIP

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

Language: Jupyter Notebook - Size: 595 MB - Last synced at: 6 days ago - Pushed at: 7 months ago - Stars: 97 - Forks: 16

zjunlp/OntoProtein

[ICLR 2022] OntoProtein: Protein Pretraining With Gene Ontology Embedding

Language: Python - Size: 650 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 146 - Forks: 22

GauravPandeyLab/ensemble_integration

Integrating multimodal data through heterogeneous ensembles

Language: Python - Size: 44.3 MB - Last synced at: 18 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 5

AlfredoBaione/protein-function-classification

Machine learning techniques to predict the functions of proteins based on their sequences.

Language: R - Size: 433 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

idrblab/AnnoPRO

Feature map and function annotation of Proteins

Language: Python - Size: 4.01 MB - Last synced at: 9 days ago - Pushed at: 10 months ago - Stars: 32 - Forks: 7

bioinf-mcb/Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Language: Python - Size: 7.24 MB - Last synced at: 9 days ago - Pushed at: 4 months ago - Stars: 37 - Forks: 6

PedroMTQ/mantis

A package to annotate protein sequences

Language: Python - Size: 13 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 55 - Forks: 6

HUBioDataLab/ProtHGT

A Heterogeneous Graph Transformer (HGT)-based model for protein function prediction using biological knowledge graphs and protein language models

Language: Python - Size: 11.5 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

branchialspace/foldbender

protein graph representation

Language: Python - Size: 190 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 5 - Forks: 1

nnilayy/BioCore

Language: Jupyter Notebook - Size: 56.2 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 0

BorgwardtLab/DeepEST

Language: Python - Size: 396 KB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

psipred/FFPredGAN

Improving protein function prediction with synthetic feature samples created by generative adversarial networks

Language: Python - Size: 158 KB - Last synced at: 5 months ago - Pushed at: over 4 years ago - Stars: 22 - Forks: 5

usadellab/prot-scriber

Assigns short human readable descriptions to biological sequences or gene families using references. For this, prot-scriber consumes sequence similarity search results in tabular format (Blast or Diamond).

Language: Rust - Size: 124 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 5 - Forks: 5

HUBioDataLab/Domain2GO Fork of ervau/Domain2GO

A Python tool for predicting protein functions by associating domains with Gene Ontology terms using existing domain and GO annotation data

Language: Python - Size: 4.01 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

RG-10/RG-10.github.io

🌱🌟 My Personal Portfolio 🌟🌱

Language: JavaScript - Size: 8.54 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 1 - Forks: 0

bio-ontology-research-group/PU-GO

Predicting protein functions using positive-unlabeled ranking with ontology-based priors

Language: Python - Size: 930 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 1 - Forks: 1

aalto-ics-kepaco/GO-LTR-prediction

Protein function prediction through latent tensor reconstruction

Language: Python - Size: 14.6 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 3 - Forks: 0

ProteinEngineering-PESB2/hfbs-class-models

Developing assembled functional classifications models via optimized machine learning algorithms

Language: Python - Size: 361 MB - Last synced at: 11 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 1

Sametle06/ProFAB

A platfrom supplies various machine learning algorithms and datasets and evaluation metrics for Protein Function Prediction

Language: Python - Size: 204 MB - Last synced at: 9 days ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

anazhmetdin/GOlite

python package to train CNN and DenseNet for protein function prediction

Language: Python - Size: 593 KB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

kiharalab/Domain-PFP

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

Language: Jupyter Notebook - Size: 3.25 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

samsinai/VAE_protein_function

Protein function prediction using a variational autoencoder

Language: Jupyter Notebook - Size: 7.7 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 85 - Forks: 27

yourh/DeepGraphGO

DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction

Language: Python - Size: 524 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 25 - Forks: 10

amirmohan/epistatic-net

Epistatic Net is an algorithm which allows for spectral regularization of deep neural networks to predict biological fitness functions (e.g., protein functions).

Language: Jupyter Notebook - Size: 1.05 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 15 - Forks: 2

psipred/STRING2GO

Protein function prediction based on protein-protein interaction network topology and deep maxout neural networks

Language: Python - Size: 34.2 KB - Last synced at: about 1 year ago - Pushed at: over 5 years ago - Stars: 6 - Forks: 3

Vikasdubey0551/Sequential-analysis-ANN

Classification of protein function based on their sequences with Artificial Neural Networks

Language: Jupyter Notebook - Size: 16.4 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 2 - Forks: 3

suyash-chintawar/OntoPred

An efficient attention-based approach for Protein Function Prediction using skip-gram features. Proposing two novel approaches, namely, OntoPred and OntoPredPlus capable to annotate protein sequences accurately.

Language: Jupyter Notebook - Size: 1020 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

idrblab/PFmulDL Fork of GCS-ZHN/PFmulDL

Multi-label protein function annotation

Language: Python - Size: 28.3 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 3

darcyabjones/pclust

A nextflow pipeline to cluster sets of proteins.

Language: R - Size: 1.55 MB - Last synced at: about 1 year ago - Pushed at: about 5 years ago - Stars: 2 - Forks: 1

anazhmetdin/protEncoder

python package to encode protein using different methods for machine learning

Language: Python - Size: 29.7 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 1

XinshaoAmosWang/DeepCriticalLearning

Deep Critical Learning. Implementation of ProSelfLC, IMAE, DM, etc.

Language: Python - Size: 36.8 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 28 - Forks: 4

AIMedLab/BioNEV Fork of ping-zhang/BioNEV

Graph Embedding Evaluation / Code and Datasets for "Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations"

Size: 27 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

johnnytam100/FPredX

FPredX

Language: Python - Size: 36.1 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1

cepdnaclk/e16-4yp-Automated-Protein-Function-Prediction

Automated protein function prediction is critical for the annotation of uncharacterized protein sequences, where accurate prediction methods are still required.we expect to create an accurate prediction model that assigns the best sub-graph of the gene ontology to each new protein and output a prediction score for this sub-graph and/or each predicted term .

Size: 182 KB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 2

SoliareofAstora/portfolio-Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN. This repository is for portfolio purposes only. For currently maintained version go to Małopolskie Centrum Biotechnologii repository - https://github.com/bioinf-mcb/Metagenomic-DeepFRI

Language: Python - Size: 736 KB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

ccdmb/pclust Fork of darcyabjones/pclust

A nextflow pipeline to cluster sets of proteins.

Language: Groovy - Size: 123 KB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0