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Keywords {🔍}

binding, proteins, residues, protein, annotations, predicted, predictions, article, pubmed, bindembeddl, prediction, google, scholar, fig, supplementary, cas, ligand, data, method, nucleic, sequence, table, performance, set, small, precision, methods, hbi, residue, acids, embeddings, classes, learning, experimental, metal, central, structure, reliable, recall, predict, molecules, nonbinding, probability, information, rost, biolip, ions, bind, function, nature,

Topics {✒️}

$$mcc=\frac{tp\cdot tn-fp\cdot fn}{\sqrt{ nature portfolio privacy policy nature https advertising research nature 468 nature precision=\frac{tn}{tn+ff} social media recall=\frac{tn}{tn+fp} $$precision=\frac{tp}{tp+fp} $$recall=\frac{tp}{tp+fn} embedding-based msa-free bindembed21dl tools reprints profile-based string kernels pipenn-emb ensemble net author information authors reliability index discussion embedding-based predictions semi-manually curated database cross-entropy loss function protein–protein interaction information motif-based profile-kernel58 f1=2\cdot \frac{negative protein language model ai/deep learning architecture protein–dna interface database homology-based inference sets combined homology-based inference challenge machine learning quantitative high-throughput proteomics protein-function prediction methods predictprotein—predicting protein structure outperformed msa-based predictions permissions original author dna-binding protein hmf-2 author correspondence msa-derived input features low-resolution structures 3q1q prona2020 predicts protein–dna msa-based method bindpredictml17 natural language processing full size image expert-crafted features protein–protein binding proteins typical cross-validation split machine learning method

Questions {❓}

• Although apparently blatantly underestimating precision, this crude simplification was needed to avoid over-prediction: methods only considering “what fraction of the experimental annotations is predicted?
• Common sequence variants affect molecular function more than rare variants?
• For instance, ProNA202019 focuses on predicting protein-, DNA-, or RNA-binding, both on the per-protein (does protein bind DNA or not?
• What’s in a name?

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