In an era where assembling a model of the human cell at the level of biomolecular structure and dynamics at or near atomistic resolution is no longer out of reach, cell structural bioinformatics will require a complete set of all human protein structures available for interaction with other biomolecules - the human protein structure targetome - and a pipeline of automated tools that allow quantitative analysis of millions of protein-ligand interactions. Towards this goal, we started with the sequences of 20,422 human proteins, and first selected the most representative structure for each protein from the protein database, ranking structures by coverage, depth, resolution and experimental method. To enable expansion into an entire human targetome, we docked small molecule ligands to our current set of protein structures. Using design constraints obtained by comparing structure assembly and ligand docking results obtained with challenging protein examples, we present a pipeline that incorporates experimental structures, AlphaFold predictions, multi-domain assembly using DEMO2, docking with AutoDock Vina and automated analysis of affinity and binding site location using center of mass comparisons as well as optimized clustering of ligand docking positions to classify binding pocket numbers and locations for a given protein-ligand pair, and across many proteins and many ligands. We hope that the resulting human targetome will be a useful addition to the growing toolkit of structural bioinformatics.