LIVIA Atlas: AlphaFold-Multimer protein interaction screens resolved to residues

Data behind LIVIA Atlas: AlphaFold-Multimer protein interaction screens scored with iLIS (AFM-LIS), keeping the interface and contact residues of every prediction. livia-atlas-human-proteome.zip: human proteome-wide screen. Schmid et al. (2025), doi:10.1101/2025.11.10.687652. livia-atlas-human-kinase-tf.zip: human kinase–transcription factor screen. Kim et al. (2025), doi:10.1101/2025.10.10.681672. livia-atlas-flypredictome.zip: FlyPredictome, Drosophila melanogaster. Kim et al. (2026), doi:10.64898/2026.04.14.718529. Keyed by FlyBase gene; identity.tsv maps every construct name to its gene, and sets.json marks subsets such as the fly kinase–TF screen (Kim et al. 2025). livia-atlas-{human,zebrafish,yeast,worm}-kinase-kinase.zip: kinase–kinase screens in human, zebrafish, yeast and C. elegans. livia-atlas-viral-dimers-afdb.zip: protein pairs of 2,765 viruses (1,699,288 predictions: every pair within each viral proteome, homodimers included, never across viruses) from the AlphaFold Database viral protein complexes release (EMBL-EBI, Google DeepMind, NVIDIA and collaborators, 2026; CC BY 4.0), one AlphaFold-Multimer model per pair, rescored with lis.py. Each zip is uncompressed, so the website reads single files by byte range. Inside: manifest.json, proteins.json, edges.tsv (pairs past the 10% FPR cutoff), and one bundle per protein in b/ (lis.py rows with residues, and a FASTA). Please cite the source of each screen. Version 0.1.1: FlyPredictome constructs carry the sequences that were folded and are placed on their genes by sequence; kinase–kinase screens added. Version 0.1.2: a gene whose isoforms were folded separately keeps one bundle per isoform, so a page can read the reference first: b/<gene>.zip holds the reference and an isoforms.json listing the others, each in b/<gene>~<k>.zip. Version 0.1.3: the viral screen is added. In the existing screens, scores are cut, not rounded (4 decimals in bundles, 3 in edge lists); 3,192 residue lists that the old scorer had shortened are emptied and flagged; missing scores are null; a sequence pair folded more than once is counted once, by its highest-iLIS prediction, while each screen keeps its own; and the fly kinase–kinase screen is complete (34,271 pairs; one batch had been filed with the kinase–TF screen). Known issue: in about 216 FlyPredictome batches (ligand–receptor, large-scale proteomics and other sets; not the kinase sets) residue numbers start at 0; they are being rescored for the next version. Versions were renumbered from 1.x to 0.1.x on 27 September 2026 (1.0 is 0.1.0, 1.1 is 0.1.1, 1.2 is 0.1.2); their files and DOIs are unchanged.