Getting the most out of your computational tools often comes down to proper usage. At SimBioSys our goal has always been to develop tools that are easy to use, with simple interfaces and a lot of automation. However, even though the scripts are simple, as a user you still need to know the best protocol to get the best performance.
Over the past three weeks, we have been working on the SAMPL project (http://sampl.eyesopen.com). SAMPL is a community competition to test protein and ligand modeling. This work has prompted us to formalize the “best practices” protocol for screening with eHiTS and LASSO.
The following graphic illustrates the workflow one should follow when using eHiTS or LASSO for screening databases. The main idea is that we should first try to generate the best model possible, using all available information prior to performing the screen. As with any modeling approach, testing and validating the model is an essential step prior to applying the model in a predictive way. Thus, in this workflow we have a series of “loops” which involve testing and evaluating the model at that step. Before moving to the next step you must be satisfied with the results.
We are looking for comments on this protocol, what do you like, what don’t you agree with, please add your comments. For more information, please visit our eHiTS page.