René's URL Explorer Experiment

Title: GitHub - westlake-repl/SaProt: Saprot: Protein Language Model with Structural Alphabet (AA+3Di) · GitHub

Open Graph Title: GitHub - westlake-repl/SaProt: Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

X Title: GitHub - westlake-repl/SaProt: Saprot: Protein Language Model with Structural Alphabet (AA+3Di)

Description: Saprot: Protein Language Model with Structural Alphabet (AA+3Di) - westlake-repl/SaProt

Open Graph Description: Saprot: Protein Language Model with Structural Alphabet (AA+3Di) - westlake-repl/SaProt

X Description: Saprot: Protein Language Model with Structural Alphabet (AA+3Di) - westlake-repl/SaProt

Opengraph URL: https://github.com/westlake-repl/SaProt

X: @github

direct link

Domain: github.com

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og:image:alt	Saprot: Protein Language Model with Structural Alphabet (AA+3Di) - westlake-repl/SaProt
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config	https://github.com/westlake-repl/SaProt/tree/main/config
dataset	https://github.com/westlake-repl/SaProt/tree/main/dataset
dataset	https://github.com/westlake-repl/SaProt/tree/main/dataset
example	https://github.com/westlake-repl/SaProt/tree/main/example
example	https://github.com/westlake-repl/SaProt/tree/main/example
figures	https://github.com/westlake-repl/SaProt/tree/main/figures
figures	https://github.com/westlake-repl/SaProt/tree/main/figures
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model	https://github.com/westlake-repl/SaProt/tree/main/model
output/ClinVar	https://github.com/westlake-repl/SaProt/tree/main/output/ClinVar
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scripts	https://github.com/westlake-repl/SaProt/tree/main/scripts
scripts	https://github.com/westlake-repl/SaProt/tree/main/scripts
utils	https://github.com/westlake-repl/SaProt/tree/main/utils
utils	https://github.com/westlake-repl/SaProt/tree/main/utils
weights/PLMs	https://github.com/westlake-repl/SaProt/tree/main/weights/PLMs
weights/PLMs	https://github.com/westlake-repl/SaProt/tree/main/weights/PLMs
LICENSE	https://github.com/westlake-repl/SaProt/blob/main/LICENSE
LICENSE	https://github.com/westlake-repl/SaProt/blob/main/LICENSE
README.md	https://github.com/westlake-repl/SaProt/blob/main/README.md
README.md	https://github.com/westlake-repl/SaProt/blob/main/README.md
__init__.py	https://github.com/westlake-repl/SaProt/blob/main/__init__.py
__init__.py	https://github.com/westlake-repl/SaProt/blob/main/__init__.py
environment.sh	https://github.com/westlake-repl/SaProt/blob/main/environment.sh
environment.sh	https://github.com/westlake-repl/SaProt/blob/main/environment.sh
requirements.txt	https://github.com/westlake-repl/SaProt/blob/main/requirements.txt
requirements.txt	https://github.com/westlake-repl/SaProt/blob/main/requirements.txt
README	https://github.com/westlake-repl/SaProt
MIT license	https://github.com/westlake-repl/SaProt
	https://github.com/westlake-repl/SaProt#saprot-protein-language-modeling-with-structure-aware-vocabulary-aa3di
	https://www.biorxiv.org/content/10.1101/2023.10.01.560349v3
	https://huggingface.co/westlake-repl/SaProt_650M_AF2
	https://portal.valencelabs.com/blogs/post/saprot-protein-language-modeling-with-structure-aware-vocabulary-uyLPrUZqyDF60Yr
	https://zhuanlan.zhihu.com/p/664754366
	https://github.com/westlake-repl/SaProt#-note-saprot-35m-and-650m-requires-structural-sa-token-input-for-optimal-performance-its-aa-only-sequence-mode-works-but-should-be-finetuned---its-frozen-embeddings-work-only-for-sa-input-not-aa-sequences-in-contrast-saprot-13b-saprot_13b_af2--saprot_13b_afdb_omg_ncbi-performs-well-with-both-sa-tokens-and-aa-only-sequences-however-with-high-quality-structural-input-saprot-is-expected-to-surpass-esm2-and-its-own-aa-only-mode-in-most-tasks
SaProt: Protein Language Modeling with Structure-aware Vocabulary	https://openreview.net/forum?id=6MRm3G4NiU
ColabSaprot v2	https://colab.research.google.com/github/westlake-repl/SaprotHub/blob/main/colab/SaprotHub_v2.ipynb?hl=en
SaprotHub	https://huggingface.co/SaProtHub
Go	https://github.com/westlake-repl/SaprotHub
wet-lab results	https://drive.google.com/file/d/1ZcDl0XYksTcUEaCfPI0tuEVo5CA031dg/view
here	https://x.com/duguyuan/status/1897101692665258245
News	https://github.com/westlake-repl/SaProt#News
Overview	https://github.com/westlake-repl/SaProt#Overview
Environment installation	https://github.com/westlake-repl/SaProt#Environment-installation
Prepare the SaProt model	https://github.com/westlake-repl/SaProt#Prepare-the-SaProt-model
Model checkpoints	https://github.com/westlake-repl/SaProt#Model-checkpoints
New experimental results	https://github.com/westlake-repl/SaProt#New-experimental-results
Load SaProt	https://github.com/westlake-repl/SaProt#Load-SaProt
Hugging Face model	https://github.com/westlake-repl/SaProt#Hugging-Face-model
Load SaProt using esm repository	https://github.com/westlake-repl/SaProt#Load-SaProt-using-esm-repository
Convert protein structure into structure-aware sequence	https://github.com/westlake-repl/SaProt#Convert-protein-structure-into-structure-aware-sequence
Predict mutational effect	https://github.com/westlake-repl/SaProt#Predict-mutational-effect
Get protein embeddings	https://github.com/westlake-repl/SaProt#Get-protein-embeddings
Perform protein inverse folding	https://github.com/westlake-repl/SaProt#Perform-protein-inverse-folding
Prepare dataset	https://github.com/westlake-repl/SaProt#Prepare-dataset
Pre-training dataset	https://github.com/westlake-repl/SaProt#Pre-training-dataset
Downstream tasks	https://github.com/westlake-repl/SaProt#Downstream-tasks
Pre-train SaProt	https://github.com/westlake-repl/SaProt#Pre-train-SaProt
Fine-tune SaProt	https://github.com/westlake-repl/SaProt#Fine-tune-SaProt
Evaluate zero-shot performance	https://github.com/westlake-repl/SaProt#Evaluate-zero-shot-performance
Citation	https://github.com/westlake-repl/SaProt#Citation
	https://github.com/westlake-repl/SaProt#news
here	https://www.nature.com/articles/s41587-025-02859-7
SaprotHub	https://www.biorxiv.org/content/10.1101/2024.05.24.595648v5
HuggingFace 1.3B-AF2	https://huggingface.co/westlake-repl/SaProt_1.3B_AF2
HuggingFace 1.3B-AF2+OMG+NCBI	https://huggingface.co/westlake-repl/SaProt_1.3B_AFDB_OMG_NCBI
Go	https://github.com/westlake-repl/SaprotHub
here	https://github.com/westlake-repl/SaProt#proteingym-benchmark
issue #23	https://github.com/westlake-repl/SaProt/issues/23
example	https://github.com/westlake-repl/SaProt#predict-mutational-effect
SaProt 35M model	https://huggingface.co/westlake-repl/SaProt_35M_AF2
35M residue-sequence-only version of SaProt	https://huggingface.co/westlake-repl/SaProt_35M_AF2_seqOnly
	https://github.com/westlake-repl/SaProt#overview
	https://github.com/westlake-repl/SaProt/blob/main/figures/pipeline.png
	https://github.com/westlake-repl/SaProt#environment-installation
	https://github.com/westlake-repl/SaProt#create-a-virtual-environment
	https://github.com/westlake-repl/SaProt#install-packages
	https://github.com/westlake-repl/SaProt#prepare-the-saprot-model
esm github	https://github.com/facebookresearch/esm
	https://github.com/westlake-repl/SaProt#model-checkpoints
SaProt_35M_AF2	https://huggingface.co/westlake-repl/SaProt_35M_AF2
SaProt_650M_PDB	https://huggingface.co/westlake-repl/SaProt_650M_PDB
SaProt_650M_AF2	https://huggingface.co/westlake-repl/SaProt_650M_AF2
SaProt_1.3B_AFDB_OMG_NCBI	https://huggingface.co/westlake-repl/SaProt_1.3B_AFDB_OMG_NCBI
	https://github.com/westlake-repl/SaProt#new-experimental-results
	https://github.com/westlake-repl/SaProt#35m-model
	https://github.com/westlake-repl/SaProt#650m--model
	https://github.com/westlake-repl/SaProt#alphafold2-vs-esmfold
	https://github.com/westlake-repl/SaProt#proteingym-benchmark
checkpoint	https://huggingface.co/westlake-repl/SaProt_650M_AF2
	https://github.com/westlake-repl/SaProt/blob/main/figures/proteingym_benchmark.jpg
	https://github.com/westlake-repl/SaProt/blob/main/figures/proteingymofficial.png
	https://github.com/westlake-repl/SaProt#load-saprot
	https://github.com/westlake-repl/SaProt#hugging-face-model
	https://github.com/westlake-repl/SaProt#load-saprot-using-esm-repository
esm	https://github.com/facebookresearch/esm
	https://github.com/westlake-repl/SaProt#convert-protein-structure-into-structure-aware-sequence
foldseek	https://github.com/steineggerlab/foldseek
here	https://drive.google.com/file/d/1B_9t3n_nlj8Y3Kpc_mMjtMdY0OPYa7Re/view?usp=sharing
	https://github.com/westlake-repl/SaProt#predict-mutational-effect
	https://github.com/westlake-repl/SaProt#get-protein-embeddings
	https://github.com/westlake-repl/SaProt#perform-protein-inverse-folding
	https://github.com/westlake-repl/SaProt#prepare-dataset
	https://github.com/westlake-repl/SaProt#pre-training-dataset
here	https://huggingface.co/datasets/westlake-repl/AF2_UniRef50
	https://github.com/westlake-repl/SaProt#downstream-tasks
here	https://drive.google.com/drive/folders/11dNGqPYfLE3M-Mbh4U7IQpuHxJpuRr4g?usp=sharing
	https://github.com/westlake-repl/SaProt#pre-train-saprot
pre-training dataset	https://huggingface.co/datasets/westlake-repl/AF2_UniRef50
	https://github.com/westlake-repl/SaProt#fine-tune-saprot
	https://github.com/westlake-repl/SaProt#record-the-training-process-optional
	https://github.com/westlake-repl/SaProt#evaluate-zero-shot-performance
	https://github.com/westlake-repl/SaProt#citation
	https://github.com/westlake-repl/SaProt#other-resources
Evolla	https://www.biorxiv.org/content/10.1101/2025.01.05.630192v1
online server	http://www.chat-protein.com/
ProTrek	https://www.biorxiv.org/content/10.1101/2024.05.30.596740v2
online server	http://search-protrek.com/
Pinal	https://www.biorxiv.org/content/10.1101/2024.08.01.606258v2
online server	http://www.denovo-pinal.com/
SaprotHub	https://www.biorxiv.org/content/10.1101/2024.05.24.595648v5
online server	https://colab.research.google.com/github/westlake-repl/SaprotHub/blob/main/colab/SaprotHub_v2.ipynb?hl=en
protein-structure	https://github.com/topics/protein-structure
protein	https://github.com/topics/protein
representation-learning	https://github.com/topics/representation-learning
protein-sequence	https://github.com/topics/protein-sequence
predicted-structures	https://github.com/topics/predicted-structures
pretraining	https://github.com/topics/pretraining
structure-aware	https://github.com/topics/structure-aware
protein-language-model	https://github.com/topics/protein-language-model
alphafold2	https://github.com/topics/alphafold2
foldseek	https://github.com/topics/foldseek
structural-alphbet	https://github.com/topics/structural-alphbet
protein-llm	https://github.com/topics/protein-llm
Readme	https://github.com/westlake-repl/SaProt#readme-ov-file
MIT license	https://github.com/westlake-repl/SaProt#MIT-1-ov-file
Please reload this page	https://github.com/westlake-repl/SaProt
Activity	https://github.com/westlake-repl/SaProt/activity
Custom properties	https://github.com/westlake-repl/SaProt/custom-properties
72 forks	https://github.com/westlake-repl/SaProt/forks
Report repository	https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2Fwestlake-repl%2FSaProt&report=westlake-repl+%28user%29
Releases	https://github.com/westlake-repl/SaProt/releases
Packages 0	https://github.com/orgs/westlake-repl/packages?repo_name=SaProt
Please reload this page	https://github.com/westlake-repl/SaProt
Please reload this page	https://github.com/westlake-repl/SaProt
Contributors	https://github.com/westlake-repl/SaProt/graphs/contributors
Please reload this page	https://github.com/westlake-repl/SaProt
Python 100.0%	https://github.com/westlake-repl/SaProt/search?l=python
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Privacy	https://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Security	https://github.com/security
Status	https://www.githubstatus.com/
Community	https://github.community/
Docs	https://docs.github.com/
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