ArticleFrontiers in bioinformatics2022
Nearest neighbor search on embeddings rapidly identifies distant protein relations.
Article in Frontiers in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 41 citations in OpenAlex.
- Article
- Advances in Protein Function Prediction from the Fifth CAFA Challenge.bioRxiv : the preprint server for biology · 2026Article
- Identifying microbial protease allergens through protein language model-guided homology.Cell systems · 2026Article
- Protein embeddings and local alignments.Computational and structural biotechnology journal · 2026Article
- Evaluating the significance of embedding-based protein sequence alignment with clustering and double dynamic programming for remote homology.Scientific reports · 2025Article
- NEAR: neural embeddings for amino acid relationships.Bioinformatics (Oxford, England) · 2025Article
- NEAR: Neural Embeddings for Amino acid Relationships.bioRxiv : the preprint server for biology · 2025Article
- Learning maximally spanning representations improves protein function annotation.bioRxiv : the preprint server for biology · 2025Article
- Major advances in protein function assignment by remote homolog detection with protein language models - A review.Current opinion in structural biology · 2025Review
- CATHe2: Enhanced CATH superfamily detection using ProstT5 and structural alphabets.Biology methods & protocols · 2025Article
- Semantic search using protein large language models detects class II microcins in bacterial genomes.mSystems · 2024Article
- Protein domain embeddings for fast and accurate similarity search.Genome research · 2024Article
- Assessing the role of evolutionary information for enhancing protein language model embeddings.Scientific reports · 2024Article
- Artificial Intelligence Learns Protein Prediction.Cold Spring Harbor perspectives in biology · 2024Review
- Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.bioRxiv : the preprint server for biology · 2024Article
- Fine-tuning protein embeddings for functional similarity evaluation.Bioinformatics (Oxford, England) · 2024Article
- Article
- Protein embedding based alignment.BMC bioinformatics · 2024Article
- nail: software for high-speed, high-sensitivity protein sequence annotation.bioRxiv : the preprint server for biology · 2024Article
- Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone.Bioinformatics (Oxford, England) · 2024Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Since 1992, all state-of-the-art methods for fast and sensitive identification of evolutionary, structural, and functional relations between proteins (also referred to as "homology detection") use sequences and sequence-profiles (PSSMs). Protein Language Models (pLMs) generalize sequences, possibly capturing the same constraints as PSSMs, e.g., through embeddings. Here, we explored how to use such embeddings for nearest neighbor searches to identify relations between protein pairs with diverged sequences (remote homology detection for levels of <20% pairwise sequence identity, PIDE). While this approach excelled for proteins with single domains, we demonstrated the current challenges applying this to multi-domain proteins and presented some ideas how to overcome existing limitations, in principle. We observed that sufficiently challenging data set separations were crucial to provide deeply relevant insights into the behavior of nearest neighbor search when applied to the protein embedding space, and made all our methods readily available for others.
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