Docking & virtual screening @home – preview

Way too many things have been happening lately, I didn’t have the time as I’d like to write new entries, one of them is the start of a new Job within the next few days 😀 [That’s a valid excuse, isn’t it?]

Anyway, a bit more complex and especially CPU/GPU heavy task is docking and receptor modelling. It depends though on what you think you want to do –

Do you just want to dock the occasional molecule(s), maybe make a nice picture, then you should be fine with a low-spec configuration as described in my post Part 1 of Drug Research @home . If you intend to do high throughput virtual screening of tens or even hundreds of thousands of compounds, you either have to have a lot of patience (in the range of days to weeks) or a lot of money for a cluster [I am not going into the possibility of using cloud-services (yet), though that would probably be an option as well].

The system I will describe is AutoDock, resp. Vina, the simplest and most “open-sourced” docking software, and combine it with other free tools for visualization, respectively preparation.

As time/computational reference: Docking a single molecule with Vina on an average modern i7 system takes ca 20-30 seconds. That’s ok for several hundreds at once. While I previously had access to Xeon based Linux Cluster, I screened 80k compounds on 12 CPUs in 10 or so days…. (well, it was a queue system shared with other users, though the way the system was set up it was more or less constantly calculation,).

Now, using Vina isn’t new and there are descriptions out there, but few deal (if at all) with automation. Furthermore, you have to pick bits and pieces from different places and combine them, which isn’t as obvious as one might think if you aren’t an expert (well, at least I don’t consider myself one in this particular field).

Until soon!