[Product Releases]

• eHiTS 2009
• Score 2009
• LASSO 2009
• CheVi
• SPROUT
• ARChem
• CAESA
• CLiDE v3.0

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[News]

Can we trust docking results?
Sept 2010

IBM Systems and Technology Group releases a white paper with eHiTS and Cell
Oct 2008

EPA's ToxCast^TM project will use SimBioSys' eHiTS as docking engine
Nov, 2007

[Events]

240th ACS
Aug 22-26, 2010
Boston, MA, USA
booth #945
see >> more

SimBioSys Quarterly Newsletter

Spring / Summer 2008
Double Issue

In this issue of the SimBioSys Quarterly Newsletter:

1. A Message from Dr. Z.Zsoldos, CSO, SimBioSys
2. Dan's tips and tricks
3. Events this summer
4. Science corner
5. News
6. New product releases
7. Technology corner
8. User publications

1.  A Message from Dr. Z. Zsoldos, CSO, SimBioSys

So, the theme of the era was Acceleration, or maybe I should borrow another phrase from the Highlander films: the Quickening – if you’ve seen the movie then you’ll know that lightning strikes the winner of the battle giving him the extra energy for eternal life. That is the feeling we shared with those who saw the system running at Bio-IT. The medical meaning of the phrase WHAT PHRASE..the Quickening? (first motion of the fetus during a pregnancy) is also appropriate as we are giving birth to eHiTS Lightning. At Bio-IT, we were a finalist, in the top three, for the Best in Show award. The general feedback was “Wow!”

http://www.simbiosys.com/blog/2008/05/01/the-wow-factor-at-the-bio-it-world-expo/

I won't belabor the details of how we accelerated eHiTS relative to Intel processors since I have discussed that in detail on the SimbioSys blog . Suffice to say we have delivered 30-50X on the PlayStation3 platform and 50-117X on an IBM QS 20 Blade. Since the show we have been busy turning some of the speed advantage into even better accuracy - mind you we never had to play catch-up in that area, but we want to jump far in the lead beyond the reach of the competitors ;-).

Where to from here? We have even more conferences coming up in the next few months. We will be holding a roundtable discussion for invited participants just prior to the CHI meeting in Boston in June. This roundtable meeting will invite thought leaders to bring their insight to bear on the design of an optimal docking solution. You can see more details of this round-table in the events section. Now we have speed on our side with accelerated docking on the Cell processor. Our algorithms are well proven for accuracy in many comparisons. While I have ideas about where to take our product line, not only eHiTS, in the future this roundtable will afford us the opportunity to get direct feedback during a peer-based discussion with our users. I'll report back on how it goes. I look forward to meeting some of you at conferences and hope you will sign up to read our blog where I am starting to discuss some of the more challenging issues in this domain.

Enjoy the rest of the newsletter – there are plenty of interesting and useful articles inside.

Have a safe and happy summer !

ZZ

2. Dan's tips and hints:

3. Upcoming events this summer:

Please contact us up-front to meet our scientists at these events:

• CHI's Structure-Based Drug Design conference, Boston, June 25-27, 2008, with a pre-meeting for Docking and Screening Roundtable, see invitation and agenda

• Drug Discovery Design & Planning Methods, Oxford, UK, July 14-18, 2008

• 3DSig: Structural Bioinformatics & Computational Biophysics, Toronto, July 18-19, 2008

• 236^th ACS, Philadelphia, PA, USA, Aug 17-21, 2008

For more details, please see our events page:
http://www.simbiosys.com/science/presentations/events.html

4. Science Corner:

* eHiTS case study with Nicotinic Acetocholine Receptors
http://www.simbiosys.com/support/eHiTS_presentation_for_nicotinic_receptors.pdf

* Protonation states and docking
http://www.simbiosys.com/blog/2008/05/17/correct-protonation-state-for-docking/

* How to ensure a fair comparison between docking solutions...
http://www.simbiosys.com/blog/2008/05/26/ cognate-docking-accuracy-measurement-vs-pre-optimized-pose/

5. News:

* The wow factor at the BIO-IT World Expo
http://www.simbiosys.com/blog/2008/05/01/the-wow-factor-at-the-bio-it-world-expo/
http://www.simbiosys.com/blog/2008/05/29/video-games-are-enabling-life-sciences-research/

* BIO IT world's Best of Show Award
http://www.simbiosys.com/blog/2008/06/09/ bio-it-worlds-2008-best-of-show-competition-in-the-press/

* Dan Harris joined SimBioSys
http://www.simbiosys.com/blog/2008/04/18/dan-harris-joined-simbiosys/

6. Product release:

* ARChem is now available with a demo version of the CrossFire Beilstein reaction database
http://www.simbiosys.com/blog/2008/05/30/29/

7.  Technology corner:

* Compare Cell/B.E., GPU and FPGA
http://www.simbiosys.com/blog/2008/05/03/ the-fast-and-the-furious-compare-cellbe-gpu-and-fpga/

* The future of HPC
http://www.simbiosys.com/blog/2008/05/29/the-future-of-hpc/

* Floating point errors
http://www.simbiosys.com/blog/2008/05/28/floating-point-errors/

* The Quality of Chemistry Software
http://www.simbiosys.com/blog/2008/06/04/chemical-software-quality-3-polar-surface-area/

8. User publications:

Two users groups have recently had publications with eHiTS results. Congratulations to them!

N. Schormann, O. Senkovich, K. Walker, D.L. Wright, A.C. Anderson, A. Rosowsky, S. Ananthan, B. Shinkre, S. Velu, D. Chattopadhyay
Proteins: Structure, Function, and Bioinformatics: "Structure-based approach to pharmacophore identification, in silico screening, and three-dimensional quantitative structure-activity relationship studies for inhibitors of Trypanosoma cruzi dihydrofolate reductase function"
PROTEINS June 2008 [Epub ahead of print - Early View]

Aldo Segura-Cabrera, Mario A. Rodriguez-Perez: "Structure-based prediction of Mycobacterium tuberculosis shikimate kinase inhibitors by high-throughput virtual screening"
Bioorganic & Medicinal Chemistry Letters, Volume 18 (2008), Issues 11, June 1 2008 pp.  3152–3157
view Article:doi:10.1016/j.bmcl.2008.05.003

For details see:
http://www.simbiosys.com/science/user_pubs/index.html

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