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Derivation and analysis of fragment libraries of protein structures

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4 Author(s)
In-Yee Lee ; Inst. of Inf. Sci., Nat. Taiwan Univ., Taipei, Taiwan ; Ta-Tsen Soong ; Jan-Ming Hoo ; Ming-Jing Hwang

Fragment assembly is attracting intense research interest as a means of predicting protein structure from sequences. Success requires a good library of local structures (i.e. fragments) to serve as building blocks for whole protein reconstruction. Here, we describe a novel two-stage clustering scheme for identifying recurrent local structures and deriving fragment libraries. Parameters that represent cluster compactness, distinctiveness, and coverage were used for evaluating library quality. According to test results, our system was capable of approximating protein structures with smaller library sets at a level of accuracy comparable to or better than methods previously reported by others.

Published in:

Bioinformatics and Bioengineering, 2004. BIBE 2004. Proceedings. Fourth IEEE Symposium on

Date of Conference:

19-21 May 2004