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JEN-HUI WANG, CHANG-BIAU YANG+ AND CHIOU-TING TSENG
Department of Computer Science and Engineering
National Sun Yat-sen University
Kaohsiung, 804 Taiwan
Given an amino acid sequence with the £\-carbon 3D coordinates on its backbone,
the all-atom protein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates
of all major atoms (N, C and O atoms) on the backbone. In this paper, we first
build a 4-residue fragment library extracted from PDB. Then, to solve PBRP, we search
for fragments with similar structures based on the inner distances. To test the performance
of our method, we use two testing sets of target proteins, one was proposed by
Maupetit et al. and the other is a subset extracted from CASP7. We compare the experimental
results of our method with three previous works, MaxSprout, Adcock's method
and SABBAC proposed by Maupetit et al. The reconstruction accuracy of our method is
comparable to these previous works. And the solution of our method is more stable than
the previous works in most target proteins. These previous works contain complicated
energy computation, while our method does not. Thus, our method requires much less
execution time than the previous works.
Received April 19, 2008; revised May 19, 2009; accepted July 10, 2009.
Communicated by Nancy M. Amato.
* This research work was partially supported by the National Science Council of Taiwan under Contract NSC-
95-2221-E-110-102. A preliminary version of this paper was presented at the National Computer Symposium,
Taichung, Taiwan, Dec. 20-21, 2007.
+ Corresponding author: cbyang@cse.nsysu.edu.tw.