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Tag: alignment/sequence-based
14 items with this tag.
Apr 21, 2026
CDR representations segregate into distinct clusters
protein-language-models/antibodies
antibody-structure-prediction
alignment/sequence-based
Apr 21, 2026
Distance between averaged PLM embeddings does not correlate with structural difference
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
Encoder-decoder PLM embeddings are better able to distinguish nearest neighbors than encoder-only PLMs
alignment/sequence-based
Apr 21, 2026
HMMs cannot identify remote homologs
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
Larger PLMs are better at homolog detection
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
PLM embeddings contain enough information to align proteins without fine-tuning
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
PLM-based sequence searches outperform sequence- and matches structure-based search methods
tm-score
protein-language-models/representations
alignment/sequence-based
alignment/structure-based
Apr 21, 2026
PLM-derived antibody representations can distinguish engineered from human-derived Abs
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
PLMs cluster antibodies from the same repertoire by V gene and maturation status
protein-language-models/antibodies
alignment/sequence-based
Apr 21, 2026
Protein language model embeddings are more predictive of homology than catalytic efficiency
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
Structural classifications can be learned from PLM-based alignment prediction
protein-language-models/representations
alignment/sequence-based
Apr 21, 2026
Structure-derived embeddings outperform sequence-derived embeddings on LM-based alignment
protein-language-models/representations
alignment/sequence-based
alignment/structure-based
Apr 21, 2026
Template CDR retrieval using embeddings
protein-language-models/antibodies
antibody-structure-prediction/cdr
tm-score
alignment/sequence-based
Apr 21, 2026
Contrastive learning of PLM embeddings on functional annotation improves variant effect prediction and homolog detection
protein-language-models/representations
contrastive-learning
alignment/sequence-based