[jlafon]

Many have commented here on the computational challenges of enumerating, storing, and searching very large virtual libraries. While molecules can be represented and stored as strings, that's an oversimplification of the problem (from a CS perspective). Scientists often want to search these large libraries in 2D and 3D, which requires computing & storing those coordinates. It can be cost prohibitive just to store the 3D coordinates for massive virtual libraries, even for large pharmaceutical companies. We've done this for 10^10 molecules [0]. If you are reading this and find this type of problem interesting, checkout www.eyesopen.com/careers

[0] https://pubs.acs.org/doi/10.1021/acs.jcim.9b00779 "Virtual Screening in the Cloud: How Big Is Big Enough?"

[ta988]

also a molecule doesnt just have a single set of 3d coordinates. You have conformers, solvent effects that affect their conformation as well... Often in a biological system it can be a minor conformer shape that is the strongly binding one (case of taxol). If you want to compute physical properties such as NMR, VCD, ECD you need to optimize your molecules in a completely different way (quantum mechanic calculations of electron shells) than just with a simple mechanical modelling approach to just do docking... we are talking about a 1s calculation per molecule vs a 24h or more for a mid-sized molecule.