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Bioinformatics 2006 22(14):e40-e48; doi:10.1093/bioinformatics/btl225
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
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A model-based approach for mining membrane protein crystallization trials

Sitaram Asur 1, Pichai Raman 2, Matthew Eric Otey 1 and Srinivasan Parthasarathy 1,*

1 Department of Computer Science and Engineering, Ohio State University
2 Department of Biophysics, Ohio State University

*To whom correspondence should be adderessed.

Motivation: Membrane proteins are known to play crucial roles in various cellular functions. Information about their function can be derived from their structure, but knowledge of these proteins is limited, as their structures are difficult to obtain. Crystallization has proved to be an essential step in the determination of macromolecular structure. Unfortunately, the bottleneck is that the crystallization process is quite complex and extremely sensitive to experimental conditions, the selection of which is largely a matter of trial and error. Even under the best conditions, it can take a large amount of time, from weeks to years, to obtain diffraction-quality crystals. Other issues include the time and cost involved in taking multiple trials and the presence of very few positive samples in a wide and largely undetermined parameter space. Therefore, any help in directing scientists’ attention to the hot spots in the conceptual crystallization space would lead to increased efficiency in crystallization trials.

Results: This work is an application case study on mining membrane protein crystallization trials to predict novel conditions that have a high likelihood of leading to crystallization. We use suitable supervised learning algorithms to model the data-space and predict a novel set of crystallization conditions. Our preliminary wet laboratory results are very encouraging and we believe this work shows great promise. We conclude with a view of the crystallization space that is based on our results, which should prove useful for future studies in this area.

Contact: Srinivasan Parthasarathy, 693 Dreese Lab, 2015 Neil Ave, Columbus, OH-43210, USA, Email: srini{at}cse.ohio-state.edu


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