IBM/AutoPeptideML

AutoML system for building trustworthy peptide bioactivity predictors

Language: Python - Size: 48.9 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 29 - Forks: 2

tyang816/SES-Adapter

🎈 Structure-aware adapter fine-tuning PLMs, with high training speed and impressive performance (Journal of Chemical Information and Modeling 2024).

Language: Python - Size: 107 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 21 - Forks: 1

Cassie818/MsaPhylo

Learning the language of phylogeny with MSA Transformer

Language: Jupyter Notebook - Size: 40 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 2 - Forks: 0

westlake-repl/SaprotHub

Making Protein Modeling Accessible to All Biologists

Language: Jupyter Notebook - Size: 91.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 113 - Forks: 14

pengzhangzhi/faplm

FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models

Language: Python - Size: 2.49 MB - Last synced at: 1 day ago - Pushed at: about 1 month ago - Stars: 118 - Forks: 11

LLNL/protlib-designer

Integer Linear Programming for Protein Library Design

Language: Python - Size: 1.93 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 6 - Forks: 0

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: 11 days ago - Pushed at: 11 days ago - Stars: 10 - Forks: 0

westlake-repl/SaProt

Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

Language: Python - Size: 2.45 MB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 445 - Forks: 43

OpenProteinAI/openprotein-python

Simple python interface for the OpenProtein.AI REST API.

Language: Python - Size: 14.5 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 9 - Forks: 0

KCLabMTU/LMSuccSite

Improving Protein Succinylation Sites Prediction Using Features Extracted from Protein Language Model

Language: Jupyter Notebook - Size: 105 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 1 - Forks: 3

biocentral/biotrainer Fork of sacdallago/biotrainer

Development branch of sacdallago/biotrainer

Language: Python - Size: 8.78 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 0 - Forks: 0

westlake-repl/ProTrek

ProTrek: Navigating the Protein Universe through Tri-Modal Contrastive Learning

Language: Python - Size: 1.19 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 101 - Forks: 8

NREL/EvoProtGrad

Directed evolution of proteins in sequence space with gradients

Language: Jupyter Notebook - Size: 9.5 MB - Last synced at: 19 days ago - Pushed at: 10 months ago - Stars: 85 - Forks: 12

bioinfodlsu/PHIStruct

Published in Bioinformatics. Phage-host interaction prediction tool that incorporates protein structure information in representing receptor-binding proteins (RBPs). It improves performance especially for phages with RBPs that have low sequence similarity to those of known phages

Language: Jupyter Notebook - Size: 15.7 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0

pentalpha/protein_dimension_db

Datasets with embeddings and other representations for all proteins in Uniprot/Swiss-Prot

Language: Python - Size: 33.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 0

ISYSLAB-HUST/ProtFlash

ProtFlash: A lightweight protein language model

Language: Python - Size: 21.5 KB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 103 - Forks: 3

zaixizhang/PocketGen

PocketGen (Nature Machine Intelligence 24): Generating Full-Atom Ligand-Binding Protein Pockets

Language: Python - Size: 15.8 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 176 - Forks: 18

THUDM/ProteinLM

Protein Language Model

Language: Python - Size: 694 KB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 117 - Forks: 21

HySonLab/LatentDE

LatentDE: Latent-based Directed Evolution for Protein Sequence Design

Language: Python - Size: 3.04 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 26 - Forks: 0

chaohaoyuan/PAAG

Source code for Annotation-guided Protein Design with Multi-Level Domain Alignment. (KDD 2025)

Language: Python - Size: 7.74 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 1

OpenProteinAI/PoET

Inference code for PoET: A generative model of protein families as sequences-of-sequences

Language: Python - Size: 772 KB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 71 - Forks: 3

mims-harvard/SPECTRA

SPECTRA: Spectral framework for evaluation of biomedical AI models

Language: Jupyter Notebook - Size: 70.1 MB - Last synced at: 11 days ago - Pushed at: 2 months ago - Stars: 38 - Forks: 7

THUDM/MSAGPT

MSAGPT

Language: Python - Size: 1.85 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 30 - Forks: 2

yutanagano/sceptr

Highly informative TCR representation model

Language: Python - Size: 14.7 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 10 - Forks: 2

PaccMann/paccmann_proteomics

PaccMann models for protein language modeling

Language: Python - Size: 3.54 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 42 - Forks: 8

HySonLab/LANTERN

LANTERN: Leveraging Large Language Models And Transformer For Enhanced Molecular Interaction

Language: Python - Size: 492 KB - Last synced at: about 2 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

dohlee/proteinbert-pytorch

Implementation of ProteinBERT, a deep language model designed for proteins.

Language: Python - Size: 87.9 KB - Last synced at: 7 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

dohlee/deepab-pytorch

An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.

Language: Python - Size: 15.8 MB - Last synced at: 22 days ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0

KYQiu21/plmrepeat

Exploiting sequence representations derived from protein language models for repeat identification

Language: Python - Size: 16.8 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

dohlee/antiberty-pytorch

An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.

Language: Jupyter Notebook - Size: 228 KB - Last synced at: 28 days ago - Pushed at: about 1 year ago - Stars: 24 - Forks: 5

Bhattacharya-Lab/EquiPNAS

pLM-informed E(3) equivariant deep graph neural networks for protein-nucleic acid binding site prediction

Language: Python - Size: 9.05 MB - Last synced at: 5 months ago - Pushed at: about 1 year ago - Stars: 21 - Forks: 1

oxpig/CaLM

Protein language model trained on coding DNA

Language: Python - Size: 67.7 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 38 - Forks: 10

LucasDedieu/MHC1-Binding

Build a classifier that predicts if a given peptide will be presented by a specific MHC1 protein.

Language: Jupyter Notebook - Size: 766 KB - Last synced at: about 2 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

ml4bio/Dense-Homolog-Retrieval

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

Language: Python - Size: 26.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 40 - Forks: 1

bioinfodlsu/phage-host-prediction

Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted sequence properties and eliminates the need to manually extract and select features from phage sequences

Language: Jupyter Notebook - Size: 10.9 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 10 - Forks: 2

ProteinEngineering-PESB2/protein-interactions-models

Exploring protein language models and machine learning algorithms for protein interactions predictive models

Language: Python - Size: 60.2 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

KCLabMTU/LMCrot

Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified Site Predictor

Language: Python - Size: 22.5 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 2

elliothershberg/interactive-mutation-browser

In silico protein surgery using ESM.

Language: TypeScript - Size: 309 KB - Last synced at: 13 days ago - Pushed at: about 1 year ago - Stars: 18 - Forks: 1

dohlee/abyssal-pytorch

Implementation of Abyssal, a deep neural network trained with a new "mega" dataset to predict the impact of an amino acid variant on protein stability.

Language: Jupyter Notebook - Size: 154 KB - Last synced at: 21 days ago - Pushed at: about 2 years ago - Stars: 6 - Forks: 2

ShubhrangshuGhosh2000/mat_p2ip_prj

Contains code for the paper "MaTPIP: a deep-learning architecture with eXplainable AI for sequence-driven, feature mixed protein-protein interaction prediction"

Language: Python - Size: 184 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

titobabatunde/SPOT-1D-LM Fork of jas-preet/SPOT-1D-LM

SPOT-1D-LM-Extended

Language: Jupyter Notebook - Size: 17.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

KCLabMTU/pLMSNOSite

An ensemble-based approach for prediction of protein S-nitrosylation sites integrating supervised word embedding and embedding from protein language model

Language: Python - Size: 75.9 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 14 - Forks: 3

jhrcook/protein-language-models

Experimenting with protein language model predictions

Language: Python - Size: 3.91 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

biovino1/SearchEmb

Searching proteins against a database of embeddings

Language: Python - Size: 309 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

dzjxzyd/pLM4ACE

Language: Jupyter Notebook - Size: 7.18 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

elttaes/Revisiting-PLMs

Exploring Evolution-aware & free protein language models as protein function predictors

Language: Python - Size: 6.55 MB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 41 - Forks: 9

vam-sin/CATHe

Deep Learning tool trained on protein sequence embeddings from protein language models to accurately detect remote homologues for CATH superfamilies

Language: Python - Size: 63.5 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 7 - Forks: 1

salvatoreloguercio/cov2vec

cov2vec is a systematic effort to obtain SARS CoV-2 genome embeddings by encoding viral genomes with protein language models.

Language: Python - Size: 15.6 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0