in this presentation, i will briefly introduce the concept of high throughput docking (htd) and how it is used in pharmaceutical and biotech industries. a successful htd requires not only accurate description of molecular interactions, but also efficient numerical algorithms. a couple of computational methods that we have developed for docking will be discussed. they demonstrate how this practical problem can greatly benefit from relatively simple mathematical methods. i will also discuss some challenges ahead for further improving htd and general high throughput virtual screening.