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Abstract
Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comprehensively explore the dual nature of proteins that act and exist as three-dimensional (3D) machines and evolve as linear strings of one-dimensional (1D) sequences. Here, we leverage pLMs to simultaneously model both modalities in a single model. We encode protein structures as token sequences using the 3Di-alphabet introduced by the 3D-alignment method Foldseek. For training, we built a non-redundant dataset from AlphaFoldDB and fine-tuned an existing pLM (ProtT5) to translate between 3Di and amino acid sequences. As a proof-of-concept for our novel approach, dubbed Protein ‘structure-sequence’ T5 (ProstT5), we showed improved performance for subsequent, structure-related prediction tasks, leading to three orders of magnitude speedup for deriving 3Di. This will be crucial for future applications trying to search metagenomic sequence databases at the sensitivity of structure comparisons. Our work showcased the potential of pLMs to tap into the information-rich protein structure revolution fueled by AlphaFold2. ProstT5 paves the way to develop new tools integrating the vast resource of 3D predictions and opens new research avenues in the post-AlphaFold2 era.
Academic Publication Bilingual language model for protein sequence and structure
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Bilingual language model for protein sequence and structure
Abstract Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein struct...
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Abstract InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known a...
Multilingual support
This issue proposes critical multilingual expansion for the 'caveman' skill, addressing the pain point of non-English-first developers. The discussion introduces a sophisticated approach for Chines...
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What is the core focus of the research titled 'Bilingual language model for protein sequence and structure'?
This literature focuses on: Abstract Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, AlphaFold2 broke through in protein structure prediction. Now we can systematically and comp...
Are there open-source GitHub repositories related to Bilingual language model for protein sequence and structure?
Yes, open-source projects like PKU-YuanGroup/Helios (Helios: Real Real-Time Long Video Generation Model) are actively building upon these concepts.
Which startups are commercializing the technology behind Bilingual language model for protein sequence and structure?
Products like FreeCAD 1.1 are bringing this to market. Their focus is: Extremely powerful, completely free 3D CAD modeling.
What other academic literature is closely related to 'Bilingual language model for protein sequence and structure'?
Yes, highly correlated activity was mapped. An entry titled 'Bilingual language model for protein sequence and structure' discusses this: Abstract Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concur...
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Commercial Realization
Startups and Open Source tools heavily associated with the concepts explored in this paper.
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GitHubPKU-YuanGroup/Helios
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GitHubwanshuiyin/Auto-claude-code-research-in-sleep
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Product HuntFreeCAD 1.1
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Product HuntOllang DX