StrAcTable

StrAcTable[1] is a protein-ligand structure and bioactivity dataset with atomistic detail.

It combines the outputs of three previously developed tools: the ActivityFinder[2], StructureProfiler[3], and LigandExtractor[4].

ActivityFinder links structural data from the Protein Data Bank to bioactivity data from the ChEMBL database, StructureProfiler characterizes the structure quality, and LigandExtractor[4] – first discussed as an in-house tool by Flachsenberg et al. – annotates any problems with or particularities of modeled small molecules.

StrAcTable also includes methods to filter data to the highest quality for each entry, annotate quality criteria for easy subset generation, and calculate additional complex properties, such as the number of mutations in the proximity of a small molecule. The corresponding datasets, processing-related data, and additional supporting data for the publication are available for download at https://www.fdr.uni-hamburg.de/record/18244.

[1] Gutermuth, T.; Ehmki, E. S. R.; Flachsenberg, F.; Penner, P.; Hönig, S. M. N.; Harren, T.; Rarey, M. Enabling automatic generation of protein-ligand complex datasets with atomistic detail. bioRxiv 2026. DOI: https://doi.org/10.64898/2026.01.15.699426
[2] Ehmki, E. S. R.; Gutermuth, T.; Harren, T.; Kurtz, S.; Rarey, M. ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data. J Chem Inf Model 2026. DOI: https://doi.org/10.1021/acs.jcim.5c02505
[3] Meyder, A.; Kampen, S.; Sieg, J.; Fahrrolfes, R.; Friedrich, N. O.; Flachsenberg, F.; Rarey, M. StructureProfiler: an all-in-one tool for 3D protein structure profiling. Bioinformatics 2019, 35 (5), 874-876. DOI: https://doi.org/10.1093/bioinformatics/bty692
[4] Flachsenberg, F.; Ehrt, C.; Gutermuth, T.; Rarey, M. Redocking the PDB. J Chem Inf Model 2024, 64 (1), 219-237. DOI: https://doi.org/10.1021/acs.jcim.3c01573