A method is presented that allows for the calculation using density functional theory (DFT) of the tunneling conductance of single molecule junctions for thousands of junction structures. With a single scaling parameter, conductance is evaluated from clusters consisting of the molecule bonded to one Au atom at each end. Junction geometries are obtained without any constraints from ab initio molecular dynamics simulations at room temperature. This method accurately reproduces standard DFT-based conductance values for several molecular and electrode structures while reducing the computational cost by a factor of ∼400×, allowing for the conductance of tens of thousands of geometries to be computed. When applied to a pair of conjugated molecules, these large data sets quantify the effect on conductance of molecular structure or quantum chemical properties. This methodology enables reliable DFT-based conductance calculations at a negligible computational cost and opens the way to quantitative structure-conductance relationships.