# Hashing for Protein Structure Similarity Search

arXiv: https://arxiv.org/abs/2411.08286 · HTML: https://mlsanity.com/paper/2411.08286/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 32 references that are in the map.
- First posted on arXiv 13 Nov 2024.

## Builds on (most cited first, 4 of 4)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [PiFold: Toward effective and efficient protein inverse folding](https://mlsanity.com/paper/2209.12643/) (2022)
- [Contrastive Representation Learning for 3D Protein Structures](https://mlsanity.com/paper/2205.15675/) (2022)

## Abstract (arXiv)

Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional alignment-based PSSS methods, which directly calculate alignment on the protein structures, are highly time-consuming with high memory cost. Recently, alignment-free methods, which represent protein structures as fixed-length real-valued vectors, are proposed for PSSS. Although these methods have lower time and memory cost than alignment-based methods, their time and memory cost is still too high for large-scale PSSS, and their accuracy is unsatisfactory. In this paper, we propose a novel method, called underlineprunderlineotein underlinestructure underlinehashing (POSH), for PSSS. POSH learns a binary vector representation for each protein structure, which can dramatically reduce the time and memory cost for PSSS compared with real-valued vector representation based methods. Furthermore, in POSH we also propose expressive hand-crafted features and a structure encoder to well model both node and edge interactions in proteins. Experimental results on real datasets show that POSH can outperform other methods to achieve state-of-the-art accuracy. Furthermore, POSH achieves a memory saving of more than six times and speed improvement of more than four times, compared with other methods.