Crystal Structure Prediction and Condor – a match made in OMII-UK

By Matthew Habgood, CPOSS.

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From aspirin to the most sophisticated and specialised drugs, it is difficult to overstate the impact that pharmaceutical chemistry has made on modern medicine. Less widely known is that a drug’s operation is dictated by a host of solid-state properties that depend on the drug’s crystal structure. A new drug might be the silver bullet for a killer virus, but if it dissolves at the wrong rate in the human bloodstream, it may be useless - or dangerous. In legal matters, patents apply only to a single crystalline form. It’s therefore no surprise that big pharmaceutical companies and other researchers are eager for a computational technique that can predict the possible crystal structures of a molecule. Crystal-structure prediction aims to provide that technique.

Crystal-structure prediction answers the question ‘what crystal structures will an organic molecule adopt?’ Different researchers have united to break that question down into two smaller steps ‘what crystal structures could this organic molecule adopt?’, and ‘which structure is the molecule most likely to adopt?’ These two questions naturally separate the computational procedure into two steps. Firstly, the generation of a bank of structures that the molecule could adopt (usually based on very simple-to-evaluate criteria). Secondly, the calculation of a lattice energy for each structure, which can be used to estimate the structure’s stability. Determining the lattice energy of a structure presents a computational challenge, since it requires energy calculations for thousands, or tens of thousands, of possible crystal structures. One solution is to exploit a Condor pool and run individual energy calculations on the unused cycles of desktop machines – for example, unused undergraduate PCs. The spoiler is that a copious series of complications arises from the first step of the crystal-structure prediction: generating thousands of structures, distributing thousands of jobs across a Condor pool, and collecting the results as they are generated.

At UCL, OMII-UK has helped Professor Price’s group by providing a set of tools and a bespoke system that allows the group’s prediction procedure to fully exploit UCL’s Condor pool. OMII-BPEL orchestrates the workflow through which the various programs involved in crystal-structure prediction are executed and coordinated, and GridSAM handles the submission of thousands of energy-evaluation jobs to the Condor pool and the subsequent collection of the results. Meanwhile, the PlotWS webservice allows us to monitor the progress of the calculations.

The basic elements of this system have been in place since 2004. Since March 2009, an active collaboration between Professor Price’s group and OMII-UK has seen the workflow upgraded and updated. Ongoing dialogue with OMII-UK has meant that the emerging system is easier to use, less prone to failure, and allows updating of the crystal-structure prediction software that the group is continually developing. With the new workflow coming online in early November 2009, the spare cycles of UCL’s desktop machines will soon be put hard to work predicting the crystal structures of organic molecules supplied from across the country by experimental and industrial collaborators of CPOSS.

http://www.cposs.org.uk