bioinf-mcb/Metagenomic-DeepFRI

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

Language: Python - Size: 6.5 MB - Last synced: about 23 hours ago - Pushed: 1 day ago - Stars: 29 - Forks: 6

ProteinEngineering-PESB2/hfbs-class-models

Developing assembled functional classifications models via optimized machine learning algorithms

Language: Python - Size: 361 MB - Last synced: 2 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

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: 1 day ago - Pushed: 7 months ago - Stars: 921 - Forks: 263

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: 2 days ago - Pushed: 11 months ago - Stars: 84 - Forks: 12

bio-ontology-research-group/PU-GO

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

Language: Python - Size: 929 KB - Last synced: 30 days ago - Pushed: about 2 months ago - Stars: 1 - Forks: 1

idrblab/AnnoPRO

Feature map and function annotation of Proteins

Language: Python - Size: 4 MB - Last synced: 30 days ago - Pushed: 4 months ago - Stars: 18 - Forks: 7

primaryodors/primarydock

PrimaryOdors.org molecular docker.

Language: C++ - Size: 179 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 5 - Forks: 3

aalto-ics-kepaco/GO-LTR-prediction

Protein function prediction through latent tensor reconstruction

Language: Python - Size: 14.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 2 - Forks: 0

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: 123 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 5 - Forks: 4

branchialspace/foldbender

molecular graph representation

Language: Python - Size: 190 MB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

microsoft/protein-uq

Benchmarking uncertainty quantification methods on proteins.

Language: Shell - Size: 131 MB - Last synced: about 1 month ago - Pushed: 10 months ago - Stars: 17 - Forks: 1

psipred/FFPredGAN

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

Language: Python - Size: 158 KB - Last synced: 30 days ago - Pushed: over 3 years ago - Stars: 19 - Forks: 5

BorgwardtLab/DeepEST

Language: Python - Size: 396 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

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: about 11 hours ago - Pushed: over 1 year 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: 4 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

GauravPandeyLab/ensemble_integration

Integrating multimodal data through heterogeneous ensembles

Language: Python - Size: 44.3 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 5

PedroMTQ/mantis

A package to annotate protein sequences

Language: Python - Size: 12.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 50 - Forks: 6

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: 7 months ago - Pushed: 7 months ago - Stars: 2 - Forks: 0

RG-10/RG-10.github.io

🌱🌟 My Personal Portfolio 🌟🌱

Language: JavaScript - Size: 8.53 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

samsinai/VAE_protein_function

Protein function prediction using a variational autoencoder

Language: Jupyter Notebook - Size: 7.7 MB - Last synced: 7 months ago - Pushed: about 6 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: 7 months ago - Pushed: almost 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: 6 months ago - Pushed: almost 3 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: 30 days ago - Pushed: almost 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: 10 months ago - Pushed: almost 4 years ago - Stars: 2 - Forks: 3

nnilayy/CAFA-5-Protein-Function-Prediction

Language: Jupyter Notebook - Size: 260 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

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: 9 months ago - Pushed: 9 months 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: 10 months ago - Pushed: 10 months ago - Stars: 6 - Forks: 3

darcyabjones/pclust

A nextflow pipeline to cluster sets of proteins.

Language: R - Size: 1.55 MB - Last synced: 24 days ago - Pushed: over 4 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: 4 months ago - Pushed: over 2 years ago - Stars: 3 - Forks: 1

zjunlp/OntoProtein

Code and datasets for the ICLR2022 paper "OntoProtein: Protein Pretraining With Gene Ontology Embedding"

Language: Python - Size: 649 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 92 - Forks: 19

XinshaoAmosWang/DeepCriticalLearning

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

Language: Python - Size: 36.8 MB - Last synced: about 1 year ago - Pushed: over 1 year 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: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

johnnytam100/FPredX

FPredX

Language: Python - Size: 36.1 MB - Last synced: about 1 year ago - Pushed: almost 2 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: 12 months ago - Pushed: about 1 year 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: almost 1 year ago - Pushed: over 2 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: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0