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Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization. LOBSTER stands for \u201cLigand Overlays from Binding SiTe Ensemble Representatives\u201d. All ligands were derived from the PDB in a fully automated workflow, including a ligand efficiency filter. So-called ligand ensembles were assembled by aligning identical binding sites. Thus, the ligands within the ensembles are superimposed according to their experimentally determined binding orientation and conformation. Overall, 671 representative ligand ensembles comprise 3583 ligands from 3521 proteins. Altogether, 72,734 ligand pairs based on the ensembles were grouped into ten distinct subsets based on their volume overlap, for the benefit of introducing different degrees of difficulty for evaluating superposition methods. Statistics on the physicochemical properties of the compounds indicate that the dataset represents drug-like compounds. Consensus Diversity Plots show predominantly high Bemis\u2013Murcko scaffold diversity and low median MACCS fingerprint similarity for each ensemble. An analysis of the underlying protein classes further demonstrates the heterogeneity within our dataset. The LOBSTER set offers a variety of applications like benchmarking multiple as well as pairwise alignments, generating training and test sets, for example based on time splits, or empirical software performance evaluation studies. The LOBSTER set is publicly available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/doi.org\/10.5281\/zenodo.12658320\" ext-link-type=\"uri\">https:\/\/doi.org\/10.5281\/zenodo.12658320<\/jats:ext-link>\n                      , representing a stable and versioned data resource. The Python scripts are available at\n                      <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/rareylab\/LOBSTER\" ext-link-type=\"uri\">https:\/\/github.com\/rareylab\/LOBSTER<\/jats:ext-link>\n                      , open-source, and allow for updating or recreating superposition sets with different data sources.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Graphical abstract<\/jats:title>\n                    <jats:p>Simplified illustration of the LOBSTER dataset generation.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1007\/s10822-024-00581-1","type":"journal-article","created":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T10:47:27Z","timestamp":1733309247000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays"],"prefix":"10.1007","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4742-7899","authenticated-orcid":false,"given":"Sophia M. 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