NAOMInova Datasets

Here, users can download precompiled NAOMInova databases. The database of PDBbind structures was dedicated to analyzing carbonyl interaction patterns. The second database comprises 408 carbonic anhydrase structures. This database was used to analyze the interactions of carbonic anhydrase with its ligands and generate ideas for extending known ligands.

Please note that these databases are in a proprietary file format for use with the NAOMInova software.

• PDBbind version 2015, general set at https://amd.zbh.uni-hamburg.de/download/naominova/naomistar_pdbBind_noedia_08Edia.sqlite (approx. 22 GB) [1]
• Carbonic anhydrase, 408 structures at https://amd.zbh.uni-hamburg.de/download/naominova/naomistar_carboAnhydrase_08Edia.sqlite (approx. 75 MB) [2]

[1] Liu, Z.; Li, Y.; Han, L.; Li, J.; Liu, J.; Zhao, Z.; Nie, W.; Liu, Y.; Wang, R. PDB-Wide Collection of Binding Data: Current Status of the PDBbind Database. Bioinformatics 2015, 31 (3), 405-412. DOI: https://doi.org/10.1093/bioinformatics/btu626
[2] Bietz, S.; Rarey, M. SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J Chem Inf Model 2016, 56 (1), 248-259. DOI: https://doi.org/10.1021/acs.jcim.5b00588