ArticleInternational journal of molecular sciences2023
Survey of Protein Sequence Embedding Models.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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Who cites it
15 citing papers in PubMed, 28 citations in OpenAlex.
- GATSBI: improving context-aware protein embeddings through biologically motivated data splits.Bioinformatics (Oxford, England) · 2026Article
- ET-Pfam: ensemble transfer learning for protein family prediction.Bioinformatics (Oxford, England) · 2026Article
- GATSBI: Improving context-aware protein embeddings through biologically motivated data splits.bioRxiv : the preprint server for biology · 2026Article
- Quantifying uncertainty in protein representations across models and tasks.Nature methods · 2026Article
- DeepPlantAllergy: deep learning for explainable prediction of allergenicity in plant proteins.Briefings in bioinformatics · 2025Article
- Computational function prediction of bacteria and phage proteins.Microbiology and molecular biology reviews : MMBR · 2025Review
- Bridging artificial intelligence and biological sciences: a comprehensive review of large language models in bioinformatics.Briefings in bioinformatics · 2025Review
- PLMFit: benchmarking transfer learning with protein language models for protein engineering.Briefings in bioinformatics · 2025Article
- PLM-ATG: Identification of Autophagy Proteins by Integrating Protein Language Model Embeddings with PSSM-Based Features.Molecules (Basel, Switzerland) · 2025Article
- Prediction of hemolytic peptides and their hemolytic concentration.Communications biology · 2025Article
- Machine learning approaches for predicting protein-ligand binding sites from sequence data.Frontiers in bioinformatics · 2025Review
- Fine-tuning protein language models unlocks the potential of underrepresented viral proteomes.PeerJ · 2025Article
- Year 2023 in Biomedical Natural Language Processing: a Tribute to Large Language Models and Generative AI.Yearbook of medical informatics · 2024Article
- Evaluating large language models for annotating proteins.Briefings in bioinformatics · 2024Article
- Progress of the "Molecular Informatics" Section in 2022.International journal of molecular sciences · 2023Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Derived from the natural language processing (NLP) algorithms, protein language models enable the encoding of protein sequences, which are widely diverse in length and amino acid composition, in fixed-size numerical vectors (embeddings). We surveyed representative embedding models such as Esm, Esm1b, ProtT5, and SeqVec, along with their derivatives (GoPredSim and PLAST), to conduct the following tasks in computational biology: embedding the
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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.