Reconstruction of Protein Backbone with the α-carbon Coordinates

Abstract

Given an amino acid sequence with the -carbon 3D coordinates on its backbone, the all-atom pro- tein backbone reconstruction problem (PBRP) is to rebuild the 3D coordinates of all atoms (N, C and O atoms) on the backbone. In this paper, we propose a method for solving PBRP based on the homology modeling. First, we extract all consecutive 4-residue fragments from all protein structures in PDB. Each fragment is identi ed by its second, third and fourth residues. Thus, the fragments are classi ed into 8000 residue groups. In each residue group, the fragments with similar structures are clustered together. And one typical fragment is used to represent one cluster. These typical fragments form our fragment library. Then, we nd out possible candidates in the frag- ment library to reconstruct the backbone of the tar- get protein. To test the performance of our method, we use two testing sets of target proteins, one was proposed by Maupetit et al. [13] and the other is a subset extracted from CASP7. We compare the ex- perimental results of our method with three previous works, MaxSprout, Adcock's method, and SABBAC proposed by Maupetit et al.. The reconstruction ac- curacy of our method is comparable to these previous works. And the solution of our method is more sta- ble than the previous works in most target proteins. The time e ciency of our method is also satisfactory.