Protein structure estimation from NMR data by matrix completion.
Knowledge of protein structures is very important to understand their corresponding physical and chemical properties. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the main methods to measure protein structure. In this paper, we propose a two-stage approach to calculate the structure of a protein from a highly incomplete distance matrix, where most data are obtained from NMR. We first randomly "guess" a small part of unobservable distances by utilizing the triangle inequality, which is crucial for the second stage. Then we use matrix completion to calculate the protein structure from the obtained incomplete distance matrix. We apply the accelerated proximal gradient algorithm to solve the corresponding optimization problem. Furthermore, the recovery error of our method is analyzed, and its efficiency is demonstrated by several practical examples.
Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, 100081, China.
Zhicheng
Z
Li
Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, 100081, China.
Yang
Y
Li
Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, 100081, China.
Qiang
Q
Lei
Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, 100081, China. qzhaoyuping@bit.edu.cn.
Qing
Q
Zhao
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins
Matrix completion; Protein structure calculation; The two-stage method