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Prokaryote translation is a complex, highly coordinated process that converts genetic information from mRNA into functional proteins. It involves three stages: initiation, elongation, and termination, each facilitated by specific molecular components.Initiation of TranslationThe process begins with the assembly of the ribosomal subunits and initiation factors on the mRNA. In bacteria, the 30S ribosomal subunit recognizes the Shine-Dalgarno sequence in the mRNA, a conserved region upstream of...
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Protein2Text: Resampling Mechanism to Translate Protein Sequences into Human-Interpretable Text.

Ala Jararweh1,2, Oladimeji Macaulay2, David Arredondo2

  • 1Department of Computer Science, The University of New Mexico.

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Protein2Text, a novel multimodal large language model, interprets protein sequences to generate informative text, accelerating the characterization of unstudied proteins and aiding biological research.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Artificial Intelligence in Life Sciences

Background:

  • Proteins are essential biological molecules, but most known sequences are uncharacterized due to experimental limitations.
  • Accelerating protein characterization is crucial for advancing biological understanding and drug discovery.

Purpose of the Study:

  • To introduce Protein2Text, a multimodal large language model designed for interpreting protein sequences.
  • To generate informative text addressing open-ended questions about protein functions and attributes, assisting experimentalists.

Main Methods:

  • Utilized an adapted LLaVA framework integrated with a resampling mechanism to map protein sequences into a language-compatible space.
  • Trained the model on a newly curated dataset derived from PubMed articles.
  • Developed and employed four comprehensive benchmarks for rigorous evaluation, including in-domain and cross-domain assessments.

Main Results:

  • Protein2Text demonstrated superior performance in open-ended question-answering tasks compared to existing models.
  • The model effectively interprets protein sequences and generates relevant textual information.
  • Highlighted limitations in current evaluation metrics for template-based approaches, advocating for unbiased assessment.

Conclusions:

  • Protein2Text offers a powerful new tool for accelerating protein characterization and hypothesis generation in biological research.
  • The model's ability to handle complex queries and generate informative text represents a significant advancement in bioinformatics.
  • Public availability of model weights and datasets facilitates further research and development in protein informatics.