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References from Protocol for tri-modal pretraining and downstream fine-tuning of protein representations using ProteinAligner. Local targets link to admitted publications; unresolved targets remain external evidence.
A tri-modal contrastive learning framework for protein representation learning
2026 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
10.1073/pnas.2016239118 · 2021 · External reference
MFDR-DTI: multisource feature decoupling and dual-level reorganization fusion for accurate drug–target interaction prediction
10.1021/acsomega.5c13460 · 2026 · External reference
MGRL-DDI: multiview graph representation learning for accurate drug–drug interaction prediction
10.1021/acs.jcim.5c01773 · 2025 · External reference
Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing
10.1093/bioinformatics/btaf664 · 2026 · External reference
scDGG: dynamic gene graphs for enhancing clustering analysis of single-cell RNA sequencing data via spatiotemporal representations
10.1016/j.compbiolchem.2025.108483 · 2025 · External reference
Precision DNA methylation typing via hierarchical clustering of nanopore current signals and attention-based neural network
10.1093/bib/bbae596 · 2024 · External reference
Systematic comparison of genome information processing and boundary recognition tools used for genomic island detection
10.1016/j.compbiomed.2023.107550 · 2023 · External reference
HPVMD-C: a disease-based mutation database of human papillomavirus in China
10.1093/database/baac018 · 2022 · External reference
BioBERT: a pre-trained biomedical language representation model for biomedical text mining
10.1093/bioinformatics/btz682 · 2020 · External reference
Unresolved reference
2004 · External reference
ProtST: multi-modality learning of protein sequences and biomedical texts
2023 · External reference
UniProt: a worldwide hub of protein knowledge
10.1093/nar/gky1049 · 2019 · External reference
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning
10.1093/nar/gkac1077 · 2023 · External reference
Enhancing missense variant pathogenicity prediction with protein language models using VariPred
10.1038/s41598-024-51489-7 · 2024 · External reference
HotProtein: a novel framework for protein thermostability prediction and editing
2023 · External reference
AcrTransAct: pretrained protein transformer models for the detection of type I anti-CRISPR activities
2023 · External reference
UniDL4BioPep: a universal deep learning architecture for binary classification in peptide bioactivity
10.1093/bib/bbad135 · 2023 · External reference
Cell-free biosynthesis combined with deep learning accelerates de novo development of antimicrobial peptides
10.1038/s41467-023-42434-9 · 2023 · External reference
Learning inverse folding from millions of predicted structures
2022 · External reference