On Drug Design

On Drug Design

"About the blog"

Personal reflections on drug design. Research interest includes combining new technology, informatics and science in innovative ways to tackle the challenging tasks in drug discovery...as well as trying to distinguish science facts from science fiction using the power of computers...something I'll post a text on now and then...usually after having read an interesting book/paper.

Searching for E.T. in Space and Drugs in the Cloud

Cool TechnologyPosted by Jonas Boström Wed, November 18, 2015 23:06:02
This was first posted: 06/04/2013 here

A long time ago, in the state of Denmark, something unusual was going on. All the screensavers in the lab had been changed to new ones. The new ones all appeared to be identical, and they had the same purpose – to search for extraterrestrial intelligence in outer space.

I quickly learned that my Ph.D. supervisor wanted to be part of the SETI@home project. SETI@home was (and is) using screensaver technology to analyze radio signals from outer space. It is now a well-known example of distributed computing. The power of distributed computing quickly becomes apparent when analyzing stats from SETI's first three years – the project accomplished in that time what a single computer would have taken 400,000 years to do.

Within the drug discovery community, Professor Graham Richards at the University of Oxford was an early adopter. Richards and his ”Screensaver Lifesaver” project exploited idle time on 3 million PC’s, cross the globe, to dock 3.5 billion compounds in protein targets. The results from the effort still remain inconclusive however. Among other initiatives, related to drug discovery, Folding@home is probably the most well-known.

Big Pharma are late into the game. Security concerns, both real and imaginary, are/were believed to outweigh possible benefits. This reasoning may be excused since the vast amounts of proprietary data within a company are key assets. Nevertheless, times are changing. Distributed computing within Big Pharma is here – in the shape of a Cloud!


Cloud computing is a synonym for distributed computing over a network and means the ability to run a program (e.g. to search for drugs and aliens) on many connected computers at the same time. The computing resources are typically off-site, available on demand, scalable, and paid per use.

I attended an excellent meeting a few weeks ago. Joe Corkery, VP at OpenEye, gave a very interesting and balanced overview on the current state of Cloud computing in Pharma. It turns out that several Big Pharma’s recently have started to exploit the Cloud; from Virtual Screens to Electronic Lab Notebooks. But the Cloud still generates most traction amongst CROs and small biotechs, where a remotely managed and maintained IT system is seen as of greater economic benefit.

Joe Corkery left stage with a parting thought: “In a pay-per-use world, speed matters.” This observation is often over-looked; the Cloud can be extremely cost-effective when time is a priority. As an example, Joe highlighted that BMS used Amazon's services to build a research Cloud for running computationally intense PK simulations for their clinical studies. In this fashion they were able to reduce the number of enrolled pediatric subjects from 60 to 40. That’s a significant saving!

Moreover, there is now a real incentive to make software faster since one pays for the time one spends in the Cloud. An incentive for getting happy customers that is. On many occasions we, the customers, do not really ‘need’ faster software. But faster software will be cheaper-to-use software. On that note, in the area of computer-aided molecular design it is not uncommon that algorithms and software have been written by non computer scientists. These are typically people who give accuracy more attention than speed and efficiency, instead of all three. So there might be some room for efficiency improvement here…and it’s always possible to make things more efficient, right? As a consequence, speedier software may lead to new ways of using it and lead to unexpected findings. That said, I am personally not in favor of a (pay-per-use) world where there's an obvious disincentive to use the software. This presents a hindrance, small though it may be (a few bucks), that might put people off from launching that extra little investigation…that in the end would have made all the difference.

I believe the Cloud computing is going to be a game-changer. My hope is that large-scale computations will provide a springboard for new scientific achievements. That is, providing opportunities for doing things that were completely intractable before (full flexible docking using quantum chemistry, including explicit waters?!), instead of just doing a lot more of the same in the spirit of “let's switch off the brain and turn on the computers in the Cloud”.

I bet that we’ll find drugs in the Cloud before we find aliens in space. Is there anyone out there, on Earth, willing to take the bet?




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