# Aligning Proteins and Language: A Foundation Model for Protein Retrieval

arXiv: https://arxiv.org/abs/2506.08023 · HTML: https://mlsanity.com/paper/2506.08023/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 20 references that are in the map.
- First posted on arXiv 27 May 2025.

## Builds on (most cited first, 10 of 10)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [MPNet: Masked and Permuted Pre-training for Language Understanding](https://mlsanity.com/paper/2004.09297/) (2020)
- [Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigm](https://mlsanity.com/paper/2110.05208/) (2021)
- [Point-Bind & Point-LLM: Aligning Point Cloud with Multi-modality for 3D Understanding, Generation, and Instruction Following](https://mlsanity.com/paper/2309.00615/) (2023)
- [Learning 3D Representations from 2D Pre-trained Models via Image-to-Point Masked Autoencoders](https://mlsanity.com/paper/2212.06785/) (2022)
- [Generalized Radiograph Representation Learning via Cross-supervision between Images and Free-text Radiology Reports](https://mlsanity.com/paper/2111.03452/) (2021)
- [Multimodal Healthcare AI: Identifying and Designing Clinically Relevant Vision-Language Applications for Radiology](https://mlsanity.com/paper/2402.14252/) (2024)
- [Read Like a Radiologist: Efficient Vision-Language Model for 3D Medical Imaging Interpretation](https://mlsanity.com/paper/2412.13558/) (2024)
- [CliNER 2.0: Accessible and Accurate Clinical Concept Extraction](https://mlsanity.com/paper/1803.02245/) (2018)

## Abstract (arXiv)

This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron Microscopy (cryo-EM). Motivated by the recent progress of vision-language models (VLMs), we propose a CLIP-style framework for aligning 3D protein structures with functional annotations using contrastive learning. For model training, we propose a large-scale dataset of approximately 200,000 protein-caption pairs with rich functional descriptors. We evaluate our model in both in-domain and more challenging cross-database retrieval on Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) dataset, respectively. In both cases, our approach demonstrates promising zero-shot retrieval performance, highlighting the potential of multimodal foundation models for structure-function understanding in protein biology.