SimBioSys Blog

Zsolt gave a great talk at ACS with lots of enthusiastic feedback. At the SimBioSys booth he discussed, in detail, the informatics underlying his accurate scoring function. Ryan Lilien (CS, prof and MD from UofT) pointed out that several speakers in the session mentioned the importance of including a scoring term for ligand burial depth, a facet that Zsolt pointed out had been in eHiTS for some time. David Kombo of Targacept came by to comment and discuss the underlying science of the scoring function. His view was echoed by several others, that while accuracy and enrichment metrics presented were impressive, the port to the cell is what really got them ‘hot’. Why was that? Look at the speedups ZZ is getting PRE-ACS in the figure below. At the time of the ACS meeting overall Zsolt was getting about 36X speed up on the QS20 and 13X on the PS3 for total flexible ligand docking to 20-targets. He’s since then made significant improvements nearly doubling those speedups for a problem of even greater complexity. Come to his poster at BIO-IT and to Booth 319 to view the latest results. Want to rapidly dock against the proteome with supercomputer/cluster performance, do family training for robust correlations with IC50’s, and do it even on a $400 platform? Stay tuned for eHiTS Lightening on the Cell. Accurate Results in Lead Discovery As Fast as a Lightning Strike.

Hi, I’m Zsolt Zsoldos, the Chief Scientific/Technical Officer here at SimBioSys. I know the blog has been going for a few months now and I am a bit late to the party, but there has been a reason for that. I’ve been focused on meeting a particular deadline, Bio-IT in Boston next week. At Bio-IT we will be showing, for the first time, eHITS lightning. This is the port of our eHITS software to the Cell processor. I won’t describe this in detail here since we’ve done it in our White Paper already. I also spoke about it at the ACS – my presentation is online here. Take a look at slide 27 in that presentation to see the speed up achieved to date. Things have progressed since that report and I will post more details after the Bio-IT. If you happen to be coming to Bio-IT please do stop by at booth #319 to visit and see eHiTS lightning running live on a Sony Playstation3.

Z.Z.

Hi, Let me introduce myself. My name is Dan (Danni) Harris and I have just joined the passionate SimBioSys Team. I have over the course of 20+ years been involved with implementing and developing unique approaches in both structure-based and indirect design, including software development to facilitate those approaches. This includes facets of lead discovery, optimization, DMPK, predictive toxicology, bio- and chemoinformatics, investigation of protein-ligand and protein-protein interactions, and quantum chemical investigations of biochemical reaction pathways. I continue to work on several of these facets as I join the SimBiosys team to deliver (sell) and support new software lead discovery and optimization solutions on both ‘conventional’ workstations and new Cell Broadband architecture.

Over the past 20 years I’ve had the pleasure of working with many of the primary software applications in the industry and have provided feedback and guidance to the numerous development teams and vendors regarding how to improve the applications. It felt like a good time with getting directly involved with the process so joining SimBioSys is an ideal opportunity to apply my insights and help the development team here deliver an optimal product (personally I think it’s damn good as it is!!!).

Having used many other vendors software I was very happy to join a company focused on cutting-edge innovations and delivery of products driven both by customers requests as well as their own insights and expertise. Certainly the opportunity to work with the Technical Lead of SimBioSys, Zsolt Zsoldos, is exciting. It was his vision that will bring eHiTS lightning (eHiTS on the Cell) to market ahead of the innovation curve relative to other companies. Zsolt and I have already had many opinionated discussions challenging each others experience and expectations and note that we are like-minded in delivering the best solutions to market. I will be blogging in coming days about some of the new technical developments as well as feedback to Zsolt’s vibrant presentation at the 2008 ACS meeting. I hope to have some lively exchanges about the challenges of lead-discovery. I think one thing we will agree upon is that ‘having the best tools to the task’ (see figure— that’s me on the tractor) is essential to a fruitful harvest (pun intended).

The SimBioSys toolset focused on a comprehensive Fragment Based approach to ‘screening’ and synthesis is (like the picture above) is unconventional, novel, fast and accurate. Stay tuned to new developments coming this month! DLH.