protein-language-model

There are 42 repositories under protein-language-model topic.

  • westlake-repl/SaProt

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

    Language:Python35767233

  • THUDM/ProteinLM

    Protein Language Model

    Language:Python11311820

  • ISYSLAB-HUST/ProtFlash

    ProtFlash: A lightweight protein language model

    Language:Python100233

  • zaixizhang/PocketGen

    Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

    Language:Python981910

  • ml4bio/Dense-Homolog-Retrieval

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

    Language:Python854212

  • westlake-repl/SaprotHub

    SaprotHub: Making Protein Modeling Accessible to All Biologists

    Language:Jupyter Notebook694107

  • NREL/EvoProtGrad

    Directed evolution of proteins in sequence space with gradients

    Language:Jupyter Notebook68888

  • elttaes/Revisiting-PLMs

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

    Language:Python602610

  • westlake-repl/ProTrek

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

    Language:Python59358

  • OpenProteinAI/PoET

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

    Language:Python47322

  • labstructbioinf/pLM-BLAST

    Detection of remote homology by comparison of protein language model representations

    Language:Python444295

  • PaccMann/paccmann_proteomics

    PaccMann models for protein language modeling

    Language:Python40898

  • oxpig/CaLM

    Protein language model trained on coding DNA

    Language:Python381910

  • THUDM/MSAGPT

    MSAGPT

    Language:Python25812

  • HySonLab/LatentDE

    Latent-based Directed Evolution guided by Gradient Ascent for Protein Design

    Language:Python24110
  • SPECTRA

    mims-harvard/SPECTRA

    Spectral Framework For AI Model Evaluation

    Language:Roff24413

  • dohlee/antiberty-pytorch

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

    Language:Jupyter Notebook22325

  • Bhattacharya-Lab/EquiPNAS

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

    Language:Python19221

  • IBM/AutoPeptideML

    AutoML system for building trustworthy peptide bioactivity predictors

    Language:Python19530

  • elliothershberg/interactive-mutation-browser

    In silico protein surgery using ESM.

    Language:TypeScript18201

  • tyang816/SES-Adapter

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

    Language:Python15211

  • KCLabMTU/pLMSNOSite

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

    Language:Python13314

  • 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 Notebook12222

  • vam-sin/CATHe

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

    Language:Python11123

  • yutanagano/sceptr

    Simple Contrastive Embedding of the Primary sequence of T cell Receptors

    Language:Python9410

  • dzjxzyd/pLM4ACE

    Language:Jupyter Notebook7200

  • 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 Notebook6212

  • OpenProteinAI/openprotein-python

    Simple python interface for the OpenProtein.AI REST API.

    Language:Python5120

  • bioinfodlsu/PHIStruct

    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 Notebook3100

  • 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:Python3102

  • dohlee/deepab-pytorch

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

    Language:Python221

  • dohlee/proteinbert-pytorch

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

    Language:Python220

  • KCLabMTU/LMCrot

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

    Language:Python2302

  • KYQiu21/plmrepeat

    Exploiting sequence representations derived from protein language models for repeat identification

    Language:Python2100

  • KCLabMTU/LMSuccSite

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

    Language:Jupyter Notebook1112

  • salvatoreloguercio/cov2vec

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

    Language:Python1100