New Paper: Searching similar local 3D micro-environments in protein structure databases with MicroMiner

6. November 2023

Foto: Jochen Sieg

Interested in the structural change induced by single mutations? MicroMiner is a new tool that provides large-scale data on the structural details of single mutations for mutation analysis, mutation effect, and structure prediction. We extracted all examples (>250 million) of amino acid pairs in protein structures from the PDB that illustrate the structural change single mutations induce to their neighborhood. We also matched this structural information with existing measures of mutation effects, like ddG measures, to obtain mutation data sets with both the mutation effect and the structural change. 

MicroMiner takes a new perspective using residue 3D micro-environments for query search. The method allows to search for structural single mutation examples for all residues in a given protein structure mostly in just a few seconds. The tool is available interactively at https://proteins.plus/, hits can be filtered by local site RMSD and global protein similarity. In addition, MicroMiner can be combined with other tools e.g., for detecting binding sites emerging upon mutation (as we showcase in the paper).

Paper: https://doi.org/10.1093/bib/bbad357 

Webserver: https://proteins.plus 

Extracted data from PDB: https://fdr.uni-hamburg.de/record/13411 

Tool: https://uhh.de/naomi 

GitHub page: https://github.com/rareylab/microminer_utils (including structure annotations of existing mutation effect data)