PiMine

Overview

PiMine enables comparisons of protein-protein interfaces. The method screens GeoMine databases generated for known interfaces for similarities based on physicochemical and shape correspondences. It automatically detects the interfaces for a protein complex of interest. Alternatively, users can use a single chain and predicted interface as input. The scoring function can assess single-chain similarities and similarities between both chains of the matched interfaces. The tool’s output consists of a list of similarity scores for all database interfaces, a binned similarity distribution, and (optionally) alignments of the matching interfaces.

Software Availability

The command-line tool PiMine is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download PiMine, 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 PiMine. The download includes detailed documentation for generating individual Postgres databases. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Graef, J.; Ehrt, C.; Reim, T.; Rarey, M. Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J Chem Inf Model 2024, 64 (8), 3332-3349. DOI: https://doi.org/10.1021/acs.jcim.3c01462