ArticleNature communications2024
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Enzyme-mediated remodeling of the extracellular matrix and glycocalyx to enhance immunotherapy in solid tumors.Bioengineering & translational medicine · 2026Review
- A trimodal protein language model enables advanced protein searches.Nature biotechnology · 2026Article
- AlphaGEM enables precise genome-scale metabolic modelling by integrating protein structure alignment with deep-learning-based dark metabolism mining.Nature communications · 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
- OTalign: optimal transport alignment for remote protein homologs using protein language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.Cell research · 2026Article
- Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.Applied and environmental microbiology · 2026Article
- Accelerating natural product discovery with linked MS-genomics and language/transformer-based models.npj antimicrobials and resistance · 2026Article
- Article
- Scalable homology detection with ERAST.Nature biotechnology · 2026Article
- A survey of downstream applications of evolutionary scale modeling protein language models.Quantitative biology (Beijing, China) · 2026Review
- Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function.Nature plants · 2026Article
- Integrated experimental and AI innovations for RNA structure determination.Nature biotechnology · 2026Review
- Enhancing protein structure prediction: evaluating the role of amino acid physicochemical features in homology search.Briefings in bioinformatics · 2026Article
- DeepVIC: modular prediction and classification of bacterial virulence factors using protein language model embeddings.Bioinformatics advances · 2026Article
- Alternative Conformation Prediction Using Deep Learning With Multi-MSA Strategy and Structural Clustering in CASP16.Proteins · 2026Article
- Exploring the protein universe with distant similarity detection methods.Protein science : a publication of the Protein Society · 2026Review
- Classification of virulence factors based on dual-channel neural networks with pre-trained language models.PloS one · 2026Article
Corrections and comments
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
Homologous protein search is one of the most commonly used methods for protein annotation and analysis. Compared to structure search, detecting distant evolutionary relationships from sequences alone remains challenging. Here we propose PLMSearch (Protein Language Model), a homologous protein search method with only sequences as input. PLMSearch uses deep representations from a pre-trained protein language model and trains the similarity prediction model with a large number of real structure similarity. This enables PLMSearch to capture the remote homology information concealed behind the sequences. Extensive experimental results show that PLMSearch can search millions of query-target protein pairs in seconds like MMseqs2 while increasing the sensitivity by more than threefold, and is comparable to state-of-the-art structure search methods. In particular, unlike traditional sequence search methods, PLMSearch can recall most remote homology pairs with dissimilar sequences but similar structures. PLMSearch is freely available at https://dmiip.sjtu.edu.cn/PLMSearch .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.