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Bioinformatics 2008 24(13):i182-i189; doi:10.1093/bioinformatics/btn165
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Designing succinct structural alphabets

Shuai Cheng Li 1, Dongbo Bu 1,2, Xin Gao 1, Jinbo Xu 3,* and Ming Li 1,*

1David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ont. N2L 3G1, Canada, 2Institute for Computing Technology, Chinese Academy of Sciences, China and 3Toyota Technological Institute at Chicago, IL 60637, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the ‘structural alphabet’ for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments.

Results: Integer linear programming technique is applied to derive the best combination of these sequence and structural information items. This approach generates significantly more accurate and succinct structural alphabets with more than 50% improvement over the previous accuracies. With these novel structural alphabets, we are able to construct more accurate protein structures than the state-of-art ab initio protein structure prediction programs such as ROSETTA. We are also able to reduce the Kolodny's library size by a factor of 8, at the same accuracy.

Availability: The online FRazor server is under construction

Contact:scli{at}uwaterloo.ca,mli{at}uwaterloo.ca, j3xu{at}tti-c.org


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