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🚀The new version of ColabSaprot (ColabSaprot v2) is out! ColabSaprot v2 features a significant overhaul of the user interface, making it more user-friendly. (1/n) 🔗Colab link: colab.research.google.com/github/westlak… 📽️Video tutorial: youtube.com/watch?v=nmLtjl… 📜Paper: doi.org/10.1101/2024.0…

In the new version (release soon), we performed extensive wet-lab validations for ColabSaprot using both zero-shot methods and supervised training approaches to engineer various proteins. The validated targets included TDG (a uracil-N-glycosylase (UNG) variant), xylanase, vGFP.

2 of my 4 tested sequences were binders, landing me in 10th place. My modified EGFs were actually better binders than EGF! Couldn't have done it without the folks behind Raygun and ProTrek. I'll write up a blog about my strategy and experience soon! Check out their papers below!

🚀 SaprotHub Major Updates! • ColabSaprot-v2 released - easier than ever • 2 new wet lab validations added • Release Saprot 1.3B • New tools: ColabProTrek, ColabProtBerts & ColabMETL • New OPMC members 🔥 Train & share your PLMs - open for everyone! youtube.com/watch?v=nmLtjl…

ColabSaprot is really very impressive... Fine-tune a state-of-the-art protein language model by just uploading a csv of proteins and values. colab.research.google.com/github/westlak… Or download other people's models from huggingface.co/SaProtHub

🧬 ProTrek Major Update: Added: 2B+ marine proteins from GOPC Total: 2.25B+ searchable proteins Natural language protein search powered by trimodal PLM 🔍 Try now: search-protrek.com Paper: biorxiv.org/content/10.110…

We release our protein chatGPT, Evola! 🌟 chat-protein.com Evola comes in two versions: 10B & 80B. The 80B model has a 1.3B Saprot encoder & a 70B LLaMA3 decoder. Trained on 546 protein question-text pairs with an 150 billion word tokens! 💡🔬 biorxiv.org/content/10.110…

Xibin just released the 10B-version weights on our GitHub: github.com/westlake-repl/… Fine-tuning example code coming soon! 🚀 The 80B version is in training and will be released after convergence.

🚀 Update on Pinal (Natural Language➡️De novo Proteins) Model weights + demo released! 🔗 Demo: denovo-pinal.com 🌟 16B parameters, trained on 1.7B text-protein pairs. 📈 Scaling data + model size = 🔥 results! Impressive scaling! 📄 Paper: biorxiv.org/content/10.110…

ProTrek Update 🚀: search-protrek.com We've just added 700M proteins from NCBI! Now ProTrek has 3B proteins from 7 major databases – 10x larger than UniProt. Generating embeddings for 3B proteins on a single A100 GPU takes 3–4 years 😱🔬 #Bioinformatics #Proteomics

Jin recently set up a Slack group for ColabSaprot discussions. Feel free to join here: westlakeai.slack.com/?redir=%2Farch… We have recently received positive experimental results from over 10 wet labs by using ColabSaprot. Video Tutorial: youtube.com/watch?v=nmLtjl…

🚀 Update! Our latest Pinal bioRxiv now includes wet lab results. More proteins with diverse text prompt on the way. Design proteins with just text. Everyone can do protein design! Demo: denovo-pinal.com paper: biorxiv.org/content/10.110… GitHub: github.com/westlake-repl/…

first work in graduate school! Can't believe it's been a year. How lucky am I to have such excellent collaborators and advisors : )

🚨 Major Update: We’ve released ColabSeprot, the sister of ColabSaprot, featuring ESM1b, ESM2, ProTrek, ProtBert! 🎉 Fine-tune protein language models in just a few clicks—no coding required! 🧬✨ 🔗 ColabSeprot: colab.research.google.com/github/westlak… ColabPLM video: youtube.com/watch?v=nmLtjl…

Happy to see our Pinal and 310.ai’s MP4 featured in Nature News! Check it out here: denovo-pinal.com . Looking forward to seeing more future work. I told AI to make me a protein. Here’s what it came up with nature.com/articles/d4158…