Research graph
References from Protein embeddings and local alignments. Local targets link to admitted publications; unresolved targets remain external evidence.
10.1038/s41586-024-07487-w
10.1038/s41586-024-07487-w · External reference
10.1016/s0022-2836(05)80360-2
10.1016/s0022-2836(05)80360-2 · External reference
10.1093/nar/25.17.3389
10.1093/nar/25.17.3389 · External reference
10.1371/journal.pone.0141287
10.1371/journal.pone.0141287 · External reference
Scoring alignments by embedding vector similarity
10.1093/bib/bbae178 · 2024 · External reference
10.1093/bioinformatics/btr701
10.1093/bioinformatics/btr701 · External reference
22 a model of evolutionary change in proteins
1978 · External reference
Unresolved reference
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10.1101/2023.01.16.524265
10.1101/2023.01.16.524265 · External reference
ProtTrans: toward understanding the language of life through self-supervised learning
10.1109/tpami.2021.3095381 · 2021 · External reference
10.1038/s41467-021-23303-9
10.1038/s41467-021-23303-9 · External reference
10.1016/0022-2836(82)90398-9
10.1016/0022-2836(82)90398-9 · External reference
10.1101/2023.07.23.550085
10.1101/2023.07.23.550085 · External reference
Modeling aspects of the language of life through transfer-learning protein sequences
10.1186/s12859-019-3220-8 · 2019 · External reference
Unresolved reference
1992 · External reference
Seq-InSite: sequence supersedes structure for protein interaction site prediction
10.1093/bioinformatics/btad738 · 2024 · External reference
Protein embedding based alignment
10.1186/s12859-024-05699-5 · 2024 · External reference
Sensitive remote homology search by local alignment of small positional embeddings from protein language models
10.7554/elife.91415 · 2024 · External reference
10.1038/s41586-021-03819-2
10.1038/s41586-021-03819-2 · External reference
10.1093/bioinformatics/btad579
10.1093/bioinformatics/btad579 · External reference
DeepGOPlus: improved protein function prediction from sequence
10.1093/bioinformatics/btz595 · 2020 · External reference
Accurate protein function prediction via graph attention networks with predicted structure information
10.1093/bib/bbab502 · 2022 · External reference
Protein structure prediction improves the quality of amino-acid sequence alignment
10.1002/prot.26392 · 2022 · External reference
Unresolved reference
External reference
10.1038/s41592-022-01700-2
10.1038/s41592-022-01700-2 · External reference
Ankh-score produces better sequence alignments than AlphaFold3
2025 · External reference
ISPRED-SEQ: deep neural networks and embeddings for predicting interaction sites in protein sequences
10.1016/j.jmb.2023.167963 · 2023 · External reference
10.1093/nar/gku1221
10.1093/nar/gku1221 · External reference
Leveraging protein language models for accurate multiple sequence alignments
2023 · External reference
Unresolved reference
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HOMSTRAD: a database of protein structure alignments for homologous families
10.1002/pro.5560071126 · 1998 · External reference
Unresolved reference
2020 · External reference
10.1093/nar/gkab852
10.1093/nar/gkab852 · 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
10.3115/v1/d14-1162
10.3115/v1/d14-1162 · 2014 · External reference
10.18653/v1/n18-1202
10.18653/v1/n18-1202 · External reference
Unresolved reference
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10.1016/j.sbi.2023.102539
10.1016/j.sbi.2023.102539 · External reference
Unresolved reference
2021 · External reference
Unresolved reference
2021 · External reference
Nearest neighbor search on embeddings rapidly identifies distant protein relations
10.3389/fbinf.2022.1033775 · 2022 · External reference
10.1038/s41586-019-1923-7
10.1038/s41586-019-1923-7 · External reference
10.1016/0022-2836(81)90087-5
10.1016/0022-2836(81)90087-5 · External reference
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
10.1002/prot.20527 · 2005 · External reference
10.1093/nar/gky092
10.1093/nar/gky092 · External reference
10.1038/s41587-023-01773-0
10.1038/s41587-023-01773-0 · External reference
Unresolved reference
2020 · External reference
XLNet: generalized autoregressive pretraining for language understanding
2019 · External reference
