ArticleNature biotechnology2024
Protein remote homology detection and structural alignment using deep learning.
Article in Nature biotechnology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers, 1 of them a synthesis that pooled it.
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Who cites it
88 citing papers in PubMed, 1 synthesis or guideline pooled it, 142 citations in OpenAlex.
- Antimicrobial resistance crisis: could artificial intelligence be the solution?Military Medical Research · 2024Pooled it
- LoL-align: sensitive and fast probabilistic protein structure alignment.Nature methods · 2026Article
- Systematic discovery of circular permutations across the protein universe using CIRPIN.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genomic mechanism of aroma terpenoids biosynthesis in plants.Journal of advanced research · 2026Review
- Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.FEMS microbiology ecology · 2026Article
- Metal binding site alignment enables network-driven discovery of recurrent geometries across sequence-divergent proteins and drug off-targets.PLoS computational biology · 2026Article
- Benchmarking protein sequence and structure search methods for remote homology detection.Genome biology · 2026Article
- EnzymeHunter: Achieving fine-grained enzyme function prediction with a hierarchically aware contrastive learning framework.Patterns (New York, N.Y.) · 2026Article
- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
- OTalign: optimal transport alignment for remote protein homologs using protein language model embeddings.Bioinformatics (Oxford, England) · 2026Article
- ExplainBind: Explainable Physicochemical Determinants of Protein-Ligand Binding via Non-Covalent Interactions.bioRxiv : the preprint server for biology · 2026Article
- Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.Cell research · 2026Article
- Structural and immunogenic evaluation of silk proteins from Bombyx mori using advanced bioinformatics and deep learning for biomaterials applications.Journal, genetic engineering & biotechnology · 2026Article
- Inferring Local Protein Structural Similarity from Sequence Alone.Journal of chemical information and modeling · 2026Article
- From atoms to fragments: a coarse representation for efficient and functional protein design.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
- Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.International journal of molecular sciences · 2026Review
- Scalable homology detection with ERAST.Nature biotechnology · 2026Article
- Deep homology and design of proteasome chaperone proteins in Candidozyma auris.Nature communications · 2026Article
- Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function.Nature plants · 2026Article
28 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
Exploiting sequence-structure-function relationships in biotechnology requires improved methods for aligning proteins that have low sequence similarity to previously annotated proteins. We develop two deep learning methods to address this gap, TM-Vec and DeepBLAST. TM-Vec allows searching for structure-structure similarities in large sequence databases. It is trained to accurately predict TM-scores as a metric of structural similarity directly from sequence pairs without the need for intermediate computation or solution of structures. Once structurally similar proteins have been identified, DeepBLAST can structurally align proteins using only sequence information by identifying structurally homologous regions between proteins. It outperforms traditional sequence alignment methods and performs similarly to structure-based alignment methods. We show the merits of TM-Vec and DeepBLAST on a variety of datasets, including better identification of remotely homologous proteins compared with state-of-the-art sequence alignment and structure prediction methods.
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Registered trials
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.