GeoMine

Overview

GeoMine enables the automated mining of protein-ligand binding sites. Based on individually designed queries, users can search for spatial interaction patterns in huge collections of protein-ligand complexes and binding pockets. The regularly updated GeoMine database relies on the free database systems SQLite and PostgreSQL. It supports radius-based pockets (based on ligands and predicted pockets (based on DoGSite3) for query generation. The query management is based on XML (for the REST service) or JSON in the GUI mode. Its output consists of the query-based superpositions of the matched binding sites and statistics on matching points, distances, and angles.

Software Availability

We are offering GeoMine as part of our ProteinsPlus web service. Please visit https://proteins.plus, upload your protein, and choose GeoMine.

References

Diedrich, K.; Ehrt, C.; Graef, J.; Poppinga, M.; Ritter, N.; Rarey, M. User-Centric Design of a 3D Search Interface for Protein-Ligand Complexes. J Comput Aided Mol Des 2024, 38 (1), 23. DOI: https://doi.org/10.1007/s10822-024-00563-3
Graef, J.; Ehrt, C.; Diedrich, K.; Poppinga, M.; Ritter, N.; Rarey, M. Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures. J Med Chem 2022, 65 (2), 1384-1395. DOI: https://doi.org/10.1021/acs.jmedchem.1c01046
Diedrich, K.; Graef, J.; Schöning-Stierand, K.; Rarey, M. GeoMine: Interactive Pattern Mining of Protein-Ligand Interfaces in the Protein Data Bank. Bioinformatics 2021, 37 (3), 424-425. DOI: https://doi.org/10.1093/bioinformatics/btaa693