protein-language-model

There are 6 repositories under protein-language-model topic.

westlake-repl / SaProt
Saprot: Protein Language Model with Structural Alphabet
alphafold2 foldseek predicted-structures pretraining protein protein-language-model protein-sequence protein-structure representation-learning structure-aware protein-llm structural-alphbet
Language:Python 230
THUDM / ProteinLM
Protein Language Model
deep-learning pretrained-models protein-language-model transfer-learning
Language:Python 104
ISYSLAB-HUST / ProtFlash
ProtFlash: A lightweight protein language model
bioinformatics protein-language-model protein-embeddings protein-sequence pretrained-models protein-representation-learning
Language:Python 93
elttaes / Revisiting-PLMs
Exploring Evolution-aware & free protein language models as protein function predictors
alphafold function-prediction fitness-prediction alphafold2 benchmark contact-prediction multiple-sequence-alignment protein-annotation protein-classification protein-language-model pytorch stability esm1b metal-ion-binding msa-construction msa-transformer remote-homology-detection zero-shot-prediction
Language:Python 55
zaixizhang / PocketGen
Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets
generative geometric-deep-learning protein-language-model protein-ligand-interactions protein-structure
Language:Python 51
NREL / EvoProtGrad
Directed evolution of proteins in sequence space with gradients
directed-evolution huggingface mcmc protein-engineering protein-language-model
Language:Jupyter Notebook 37
PaccMann / paccmann_proteomics
PaccMann models for protein language modeling
protein-language-model transformer pytorch
Language:Python 37
OpenProteinAI / PoET
Inference code for PoET: A generative model of protein families as sequences-of-sequences
deep-learning generative-model protein-engineering protein-language-model protein-sequences proteins
Language:Python 33
oxpig / CaLM
Protein language model trained on coding DNA
codons computational-biology deep-learning dna language-models llms machine-learning protein-language-model
Language:Python 26
dohlee / antiberty-pytorch
An unofficial re-implementation of AntiBERTy, an antibody-specific protein language model, in PyTorch.
antibody-sequence antibody-sequences protein protein-language-model protein-sequences bioinformatics biology
Language:Jupyter Notebook 22
SPECTRA
mims-harvard / SPECTRA
Spectral Framework For AI Model Evaluation
benchmark-framework benchmarking foundation-models geometric-deep-learning large-language-models protein-language-model protein-sequences protein-structure
Language:Roff 22
HySonLab / LatentDE
Latent-based Directed Evolution guided by Gradient Ascent for Protein Design
directed-evolution evolutionary-algorithm gradient-ascent protein-language-model protein-optimization variational-autoencoder
Language:Python 19
elliothershberg / interactive-mutation-browser
In silico protein surgery using ESM.
protein-language-model protein-structure
Language:TypeScript 18
Bhattacharya-Lab / EquiPNAS
pLM-informed E(3) equivariant deep graph neural networks for protein-nucleic acid binding site prediction
graph-neural-netowrks protein-dna-interactions protein-language-model protein-rna-interactions
Language:Python 14
KCLabMTU / pLMSNOSite
An ensemble-based approach for prediction of protein S-nitrosylation sites integrating supervised word embedding and embedding from protein language model
protein-language-model ptm plmsnosite prot-t5 ptm-prediction s-nitrosylation
Language:Python 14
IBM / AutoPeptideML
AutoML system for building trustworthy peptide bioactivity predictors
automl biochemistry peptide-prediction protein-language-model interpretable-machine-learning trustworthy-ai
Language:Python 11
vam-sin / CATHe
Deep Learning tool trained on protein sequence embeddings from protein language models to accurately detect remote homologues for CATH superfamilies
deep-learning protein-sequences protein-language-model machine-learning proteins bioinformatics neural-networks
Language:Python 11
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
bioinformatics genomics phage-host-prediction protein protein-embedding protein-language-model proteomics representation-learning transfer-learning transformer machine-learning
Language:Jupyter Notebook 9
tyang816 / SES-Adapter
Structure-aware adapter fine-tuning PLMs, with high training speed and impressive performance.
adapter fine-tuning protein-language-model protein-structure protein-downstream-tasks
Language:Python 7
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.
bioinformatics computational-biology protein protein-language-model protein-sequences protein-stability biology deep-learning reproduction reproduction-code
Language:Jupyter Notebook 6
dzjxzyd / pLM4ACE
bioactivity peptide-prediction bioactive-pepeptide peptide peptide-features protein-language-model
Language:Jupyter Notebook 4
dohlee / proteinbert-pytorch
Implementation of ProteinBERT, a deep language model designed for proteins.
bert bert-model protein protein-language-model transformer transformers transformers-bert proteinbert
Language:Python 2
KCLabMTU / LMCrot
Protein Language Model (pLM) Powered Protein Crotonylation (Kcr) Modified Site Predictor
crotonylation natural-language-processing post-translational-modification protein-language-model protein-sequences transformers
Language:Python 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"
deep-learning-architecture explainable-ai protein-language-model protein-protein-interaction-prediction protein-sequence-features
Language:Python 2
dohlee / deepab-pytorch
An unofficial re-implementation of DeepAb, an interpretable deep learning model for antibody structure prediction.
antibody antibody-sequences bioinformatics biology computational-biology protein protein-language-model protein-structure-prediction antibody-structure-prediction
Language:Python 1
KCLabMTU / LMSuccSite
Improving Protein Succinylation Sites Prediction Using Features Extracted from Protein Language Model
plm post-translational-modification protein-language-model ptm-prediction succinylation-site-prediction embeddings succinylation
Language:Jupyter Notebook 1
OpenProteinAI / openprotein-python
Simple python interface for the OpenProtein.AI REST API.
generative-ai language-model machine-learning protein-embedding protein-language-model proteins python
Language:Jupyter Notebook 1
salvatoreloguercio / cov2vec
cov2vec is a systematic effort to obtain SARS CoV-2 genome embeddings by encoding viral genomes with protein language models.
covid-19 embeddings manifold-learning protein-language-model
Language:Python 1
ProteinEngineering-PESB2 / protein-interactions-models
Exploring protein language models and machine learning algorithms for protein interactions predictive models
deep-learning machine-learning pretrained-models protein-language-model protein-protein-interaction
Language:Python 0
titobabatunde / SPOT-1D-LM
SPOT-1D-LM-Extended
11-785 protein-language-model transfer-learning end-to-end-sequence
Language:Jupyter Notebook 0
biovino1 / SearchEmb
Searching proteins against a database of embeddings
homology-search protein-language-model structure-prediction
Language:Python
jhrcook / protein-language-models
Experimenting with protein language model predictions
data-analysis protein-language-model variant-effect-prediction
Language:Python