MicroMiner

Overview

MicroMiner assists in identifying single-residue substitutions in protein structure databases. It searches protein residue environments with local sequence and structural similarity based on the SIENA methodology. Users can search for structural mutation in the entire PDB, their in-house structure collection, or (subsets of) the AlphaFold Database. They can use the method to explore the mutation landscape of proteins with experimental or predicted structures. MicroMiner can be applied to single domains or even protein-protein or protein-ligand interfaces. Several filter options to simplify downstream analysis are available.

Software Availability

We are offering MicroMiner as part of our ProteinsPlus web service. There, users can search a database of protein structures from the PDB. Please visit https://proteins.plus, upload your protein, and choose MicroMiner.

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

References

Sieg, J.; Rarey, M. Searching Similar Local 3D Micro-Environments in Protein Structure Databases with MicroMiner. Brief Bioinform 2023, 24 (6), bbad357. DOI: https://doi.org/10.1093/bib/bbad357