SiteMine

Overview

SiteMine was developed to compare small molecule binding sites in large databases and calculate their physicochemical and shape similarity. Users can screen large GeoMine databases of ligand-based and/or predicted binding sites for similar sites to a fully automatically modeled query site. Users can create databases of individual experimental or predicted structures. A prefiltering cascade based on several pocket properties and subsets of structure identifiers reduces the number of relevant pockets before screening. Similarity calculations include two scoring functions that account for the physicochemical and shape similarities of the respective binding sites. SiteMine runs take approx. three minutes on a database of 10,000 pockets.

Software Availability

The command-line tool SiteMine is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download SiteMine, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run SiteMine. The download includes detailed documentation for generating individual Postgres databases. All feedback is highly appreciated.

References

Reim, T.; Ehrt, C.; Graef, J.; Günther, S.; Meents, A.; Rarey, M. SiteMine: Large-scale binding site similarity searching in protein structure databases. Arch Pharm (Weinheim) 2024, 357 (5), e2300661. DOI: https://doi.org/10.1002/ardp.202300661