StructureMapper is a high-throughput algorithm for automated mapping of protein primary amino sequence locations to existing three-dimensional protein structures. The algorithm is intended for facilitating easy and efficient utilization of structural information in protein characterization and proteomics. StructureMapper provides an analysis of the identified structural locations that includes surface accessibility, flexibility, protein–protein interfacing, intrinsic disorder prediction, secondary structure assignment, biological assembly information and sequence identity percentages, among other metrics.


We have showcased the use of the algorithm by estimating the coverage of structural information of the human proteome, identifying critical interface residues in DNA polymerase γ, profiling structurally protease cleavage sites and post-translational modification sites, and by identifying putative, novel phosphoswitches.

Availability and implementation

The StructureMapper algorithm is available as an online service and standalone implementation at

Supplementary information

Supplementary data are available at Bioinformatics online.

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