Large-scale quantum electronic structure calculations coupled with nonequilibrium Green function theory are employed for determining quantum conductance on practical length scales. The combination of state-of-the-art quantum mechanical methods, efficient numerical algorithms, and high performance computing allows for realistic evaluation of properties at length scales that are routinely reached experimentally. Two illustrations of the method are presented. First, quantum chemical calculations using up to 104 basis functions are used to investigate the amphoteric doping of carbon nanotubes by encapsulation of organic molecules. As a second example, we investigate the electron transport properties of a Si/organic molecule/Si junction using a numerically optimized basis.