Author:
Tasissa Abiy,Benavides Tiburon,Lai Rongjie,Wang Chunyu
Abstract
AbstractThe problem of finding the configuration of points given partial information on pairwise inter-point distances, the Euclidean distance geometry problem, appears in multiple applications. In this paper, we propose an approach that integrates structural similarity and a nonconvex distance geometry algorithm for the protein structure determination problem. When initialized with a homologous structure, reconstruction of ubiquitin structure with our non convex algorithm resulted in an RMSE of less than 2 Å with 1.5% available inter proton distance and up to 20% relative error in the input distances. To test the robustness of this algorithm with regard to initialization, we also initialized with a nonhomologous structure on a larger protein with pdb coordinate 1W2E. Even though the initialization structure 1JYB is far different from 1W2E with an RMSE of 25 Å, reconstruction generated structures with RMSE of close to 2 Å, using 1.7% available proton distances and up to 10% relative error in input distances. These results suggest EDG-based approach may be applied to fast NMR structure determination in the future.
Publisher
Cold Spring Harbor Laboratory