SimBioSys founder and CSO, Zsolt Zsoldos, who is both a mathematician / computer scientist and a chemist, was recently invited to speak at one of the Fields’ Seminars. This was a great honour and recognition of the scientific
work he does at SimBioSys with his team of exceptional and talented researchers. The title of the March 2nd, 2010 presentation was: “Algorithmic and mathematical challenges in protein-ligand docking and scoring”, which has been a significant part of Zsolt’s work in the past 10 years. He tried squeezing it into just a 1 hour session, and that alone was a huge challenge. Nevertheless, there were many sparkling eyes in the audience, and hopefully the whole topic created enough interest so that we’ll see a few more mathematicians in this challenging field of science in the future. You can check out Zsolt’s talk at: http://www.simbiosys.com/science/presentations/index.html#2010
the audio and slides of the talk will be also shortly posted at Fields Institute’s web site at: http://www.fields.utoronto.ca/audio/#optimization_seminar

Another current, and interesting talk by a SimBioSys’ scientist will be given by Orr Ravitz at the upcoming spring 2010 ACS meeting in San Francisco. He will be talking about “Improving molecular docking through eHiTS’ tunable
scoring function”, in the Drug Discovery session on Monday March 22, 2010 at 10:00 am.

Abstract: The molecular docking paradigm has been hampered by the lack of a generically well performing scoring function. We present two complementary family-based approaches for score-tuning that improve docking performance  using experimental data. One technique treats the relative weights of the eHiTS energy terms as parameters that can be adjusted to improve score-RMSD correlations. The other technique is employing ligand-based similarity to rescale the docking score such that better enrichment factors are achieved in virtual screening. We discuss the algorithmic details of the methods, and demonstrate the effects of score tuning on a variety of targets, including CDK2, BACE1 and AChBP, as well as on common benchmarks. We observe an average improvement of 10% in the top-rank pose RMSD, and a similar improvement for docking success (top pose under 2 A). An average EF(1%) of 15 is achieved for the targets in the DUD set.
http://abstracts.acs.org/chem/239nm/program/view.php?obj_id=9832&terms=

Should be a discussion starter! Please join us for the session if you’ll be at the ACS meeting in SFO in two weeks, and contact us if you would like to meet  with us during the days of the conference.
posted by Aniko

A new article in Elsevier’s Bioorganic & Medicinal Chemistry Letters describes how researchers at the University of Leeds discovered novel non-peptide leads for β-secretase (BACE-1) - one of the key enzymes involved in the pathogenesis of Alzheimer’s disease, and a major target for drug discovery.
It is particularly exciting for us to know that our tools may play an instrumental role in finding a cure for a disease that affects so many beloved people in our lives.

The paper:

When it comes to business computer systems, nothing is more mission-critical than the massive trading software systems that underlie stock markets. A failure of an hour here can mean billions of dollars of lost trades….

see article at London Stock Exchange dumps Windows for Linux

Bottom line, the London Stock Exchange (LSE) had so many troubles and scandals due to software problems (crash, slow etc.) in the past, all related to their Windows 2003-based servers, that they decided to look for a Linux replacement that seems to be more reliable, faster and a lot cheaper solution - their conterpart in the USA - the NYSE - had done so a long time ago.

I hope the pharmaceutical companies do not consider their operations less mission critical.

posted by: Aniko