ArticleBioinformatics (Oxford, England)2023
pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45 citing papers in PubMed.
- Article
- A high-confidence inventory of the proteins in the mitochondrion-related organelle of Giardia.Current biology : CB · 2026Article
- Conformational diversity in poly-HAMP arrays and its implications for signal transduction.Protein science : a publication of the Protein Society · 2026Article
- Benchmarking protein sequence and structure search methods for remote homology detection.Genome biology · 2026Article
- Decoding viral protein sequences by large language models.Briefings in bioinformatics · 2026Review
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Inferring Local Protein Structural Similarity from Sequence Alone.Journal of chemical information and modeling · 2026Article
- EMERALD-UI: an interactive web application to unveil novel protein biology hidden in the alternative alignment space.Bioinformatics (Oxford, England) · 2026Article
- pLM-Repeat: Exploiting the sequence representations of protein language models for sensitive repeat detection.Protein science : a publication of the Protein Society · 2026Article
- From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.World journal of microbiology & biotechnology · 2026Review
- Identifying microbial protease allergens through protein language model-guided homology.Cell systems · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Protein Structure Prediction Methods.Advances in experimental medicine and biology · 2026Review
- Alternative Conformation Prediction Using Deep Learning With Multi-MSA Strategy and Structural Clustering in CASP16.Proteins · 2026Article
- ADAPT: a programme for the advanced detection of AI-enabled pathogenic threats.Frontiers in bioengineering and biotechnology · 2026Article
- Protein embeddings and local alignments.Computational and structural biotechnology journal · 2026Article
- Seq2Bind webserver for binding site prediction from sequences using fine-tuned protein language models.NAR genomics and bioinformatics · 2025Article
- Protein language models uncover carbohydrate-active enzyme function in metagenomics.BMC bioinformatics · 2025Article
- Topological deep learning for enhancing peptide-protein complex prediction.Communications chemistry · 2025Article
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5 authors.
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Abstract
motivationThe detection of homology through sequence comparison is a typical first step in the study of protein function and evolution. In this work, we explore the applicability of protein language models to this task.
resultsWe introduce pLM-BLAST, a tool inspired by BLAST, that detects distant homology by comparing single-sequence representations (embeddings) derived from a protein language model, ProtT5. Our benchmarks reveal that pLM-BLAST maintains a level of accuracy on par with HHsearch for both highly similar sequences (with >50% identity) and markedly divergent sequences (with <30% identity), while being significantly faster. Additionally, pLM-BLAST stands out among other embedding-based tools due to its ability to compute local alignments. We show that these local alignments, produced by pLM-BLAST, often connect highly divergent proteins, thereby highlighting its potential to uncover previously undiscovered homologous relationships and improve protein annotation. AVAILABILITY AND IMPLEMENTATION: pLM-BLAST is accessible via the MPI Bioinformatics Toolkit as a web server for searching precomputed databases (https://toolkit.tuebingen.mpg.de/tools/plmblast). It is also available as a standalone tool for building custom databases and performing batch searches (https://github.com/labstructbioinf/pLM-BLAST).
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