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References from Paying attention to attention: High attention sites as indicators of protein family and function in language models. Local targets link to admitted publications; unresolved targets remain external evidence.
Learning the protein language: evolution, structure, and function
2021 · External reference
DeepGOPlus: improved protein function prediction from sequence
10.1093/bioinformatics/btz595 · 2020 · External reference
The promises of large language models for protein design and modeling
10.3389/fbinf.2023.1304099 · 2023 · External reference
The transformative power of transformers in protein structure prediction
10.1073/pnas.2303499120 · 2023 · External reference
Embeddings from protein language models predict conservation and variant effects
10.1007/s00439-021-02411-y · 2022 · External reference
Interpretable feature extraction and dimensionality reduction in ESM2 for protein localization prediction
2024 · External reference
Advances in the application of protein language modeling for nucleic acid protein binding site prediction
10.3390/genes15081090 · 2024 · External reference
Attention is all you need
2017 · External reference
On explaining with attention matrices
2024 · External reference
Pool PaRTI: A PageRank-based pooling method for robust protein sequence representation in deep learning
2024 · External reference
Evolutionary-scale prediction of atomic-level protein structure with a language model
10.1126/science.ade2574 · 2023 · External reference
Single-sequence protein structure prediction using a language model and deep learning
10.1038/s41587-022-01432-w · 2022 · External reference
Tree visualizations of protein sequence embedding space enable improved functional clustering of diverse protein superfamilies
10.1093/bib/bbac619 · 2023 · External reference
Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone
10.1093/bioinformatics/btad786 · 2024 · External reference
Attend first, consolidate later: On the importance of attention in different LLM layers
2024 · External reference
Language models of protein sequences at the scale of evolution enable accurate structure prediction
2022 · External reference
Aggregating residue-level protein language model embeddings with optimal transport
2024 · External reference
Efficient interactive LLM serving with proxy model-based sequence length prediction
2024 · External reference
Protein language models learn evolutionary statistics of interacting sequence motifs
10.1073/pnas.2406285121 · 2024 · External reference
Assessing the role of evolutionary information for enhancing protein language model embeddings
10.1038/s41598-024-71783-8 · 2024 · External reference
Domain-PFP allows protein function prediction using function-aware domain embedding representations
10.1038/s42003-023-05476-9 · 2023 · External reference
learnMSA: learning and aligning large protein families
10.1093/gigascience/giac104 · 2022 · External reference
RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy
10.1093/nar/gky1004 · 2019 · External reference
Protein function prediction as approximate semantic entailment
10.1038/s42256-024-00795-w · 2024 · External reference
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction
10.1002/prot.26052 · 2021 · External reference
ProteinBERT: a universal deep-learning model of protein sequence and function
10.1093/bioinformatics/btac020 · 2022 · External reference
UniProt: the universal protein knowledgebase
External reference
Light attention predicts protein location from the language of life
10.1093/bioadv/vbab035 · 2021 · External reference
10.1002/9781118445112.stat06558
10.1002/9781118445112.stat06558 · External reference
Embedding-based Silhouette community detection
10.1007/s10994-020-05882-8 · 2020 · External reference
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
10.1038/msb.2011.75 · 2011 · External reference
The active site of the SET domain is constructed on a knot
2023 · External reference
Structure and catalytic mechanism of a SET domain protein methyltransferase
10.1016/s0092-8674(02)01000-0 · 2002 · External reference
The role of Mg2 cofactor in the guanine nucleotide exchange and GTP hydrolysis reactions of rho family GTP-binding proteins.
10.1074/jbc.m001027200 · 2000 · External reference
IFN-inducible GTPases in host cell defense
10.1016/j.chom.2012.09.007 · 2012 · External reference
Molecular and biotechnological aspects of microbial proteases
10.1128/mmbr.62.3.597-635.1998 · 1998 · External reference
Serine proteases of parasitic helminths
10.3347/kjp.2015.53.1.1 · 2015 · External reference
Allostery in trypsin-like proteases suggests new therapeutic strategies
2023 · External reference
10.1109/tpami.2021.3095381
10.1109/tpami.2021.3095381 · External reference
