The protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments heavily relies on computational algorithms , such as matrix completion (MC) . Recently, some effective low-rank matrix completion methods, like ASD and ScaledASD, have been successfully applied in image processing, which inspired us to apply them in protein structure reconstruction. Here we present an efficient method for determining protein structures from experimental NMR NOESY distances , by combining the ScaledASD algorithm with several afterwards procedures including chirality refinement, distance lower (upper) bound refinement, force field-based energy minimization (EM) and water refinement. By comparing several metrics on conformation evaluation between our results and the PDBdeposits , we conclude that our method is consistent with the popular used methods. In particular, our results show higher validities in MPscore, Molprobity clash-score, Procheck dihedral angles G-factor than PDB models. In the end, we compared our calculation results with PDB models by checking the structural similarity to X-ray crystallographic structure for a special dataset. The software and its MATLAB source codes are available by URL
Protein structure reconstruction from Nuclear Magnetic Resonance (NMR) experiments largely relies on computational algorithms . Recently, some effective low-rank matrix completion (MC) methods, such as ASD and ScaledASD, have been successfully applied to image processing, which inspires us to apply the methods to reconstruct protein structures. In this paper, we present an efficient method to determine protein structures based on experimental NMR NOESY distances . ScaledASD algorithm is used in the method with several post-procedures including chirality refinement, distance lower (upper) bound refinement, force field-based energy minimization (EM) and water refinement. By comparing several metrics in the conformation evaluation on our results with Protein Data Bank (PDB) structures , we conclude that our method is consistent with the popularly used methods. In particular, our results show higher validities in Procheck dihedral angles G-factor . Furthermore, we compare our calculation results with PDB structures by examining the structural similarity to X-ray crystallographic structures in a special dataset. The software and its MATLAB source codes are available in URL
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