Protein Colour: Hard to Beat a Simple Average
A model can put proteins in a useful order while barely improving its predictions. Six rhodopsin models show why error in nanometres matters alongside rank correlation.
Tagged
#protein language models
4 articles tagged with #protein language models.
A Protein Embedding Is Not an Explanation: Protein Language Models in 2026
A practical guide to choosing, extracting, adapting and validating protein language-model representations without mistaking a system score for biological generalisation.
Structure Without Alignment: How ESM-2 Folds a Single Sequence
ESMFold predicts atomic-level structure from a single sequence. No multiple sequence alignment, no database search, no Evoformer churning over homologs.
A Bioinformatician's Guide to Choosing Genomic Foundation Models
A practical guide to selecting genomic foundation models for bioinformatics tasks. Covers ESM-2, DNABERT-2, HyenaDNA, Nucleotide Transformer, scGPT, and Evo with scoped comparisons for DNA, proteins and single-cell analysis, with corrected references and clear distinctions between frozen representations and trained predictors.
