Reconstruction of Protein Backbone with the α-Carbon Coordinates

王仁暉(Jen-Hui Wang) ； 楊昌彪(Chang-Biau Yang) ； 曾球庭(Chiou-Ting Tseng)

《Journal of Information Science and Engineering》 26卷3期 (2010/05) Pp. 1107-1119

https://doi.org/10.6688/JISE.2010.26.3.23

並列摘要

Given an amino acid sequence with the α-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.

並列關鍵字

bioinformatics ； protein structure ； backbone reconstruction ； α-carbon ； RMSD