SimBioSys Blog

One of our customers recently asked us to provide him with a short presentation explaining our retrosynthetic analysis software, ARChem, so that he would be able to advertise it to potential users within his organization. Since, to paraphrase the old adage, a clip is worth a thousand slides, we opted for a 5 minutes video.

It’s not easy to squeeze the essence of a product like ARChem into a short video, since it has so many facets: the search engine, the solutions display, solutions filtering, interfacing with reaction databases not to mention all the science that is at work under the hood. So we decided to focus on the core value of ARChem: the ability to harvest knowledge from experimental data, and to convert the knowledge to ideas. In 5 minutes we show, without discussing the fascinating underlying technology, the available search strategies, solutions viewing and construction, sharing ideas with your fellow researchers, and viewing literature examples. Please see the movie at:

http://www.simbiosys.com/archem/video/

We hope you will find it interesting.

Our article on eHiTS Tune and Score is now available online:

Improving molecular docking through eHiTS’ tunable scoring function
Journal of Computer-Aided Molecular Design
DOI: 10.1007/s10822-011-9482-5

The article contains lots of useful information about eHiTS Score and Tune algorithms, as well as it gives validation of the same using a number of test sets, including CDK2 and BACE1 for pose prediction, DUD for virtual screening and PDBBind for affinity prediction. eHiTS results are compared with other programs’ published results where such data were available. For example enrichment results on the DUD set were compared using results from Cross et.al (DOI: 10.1021/ci900056c)

In conclusion, the article states that knowledge-based approaches are mainstream methods today, because they benefit from the ever expanding base of experimental data and from continuous progress in computational methods, and that score tuning is a natural extension of that concept. The authors also hope to solicit for wider use of the score tuning methodology and creation of test sets in the user community.

See the full article here
http://www.springerlink.com/content/r1t66167718h5110/